diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
index 1de1e12694..c66c4c23c8 100644
--- a/.github/workflows/ci.yml
+++ b/.github/workflows/ci.yml
@@ -5,6 +5,8 @@ on:
     branches:
       - dev
   pull_request:
+    paths-ignore:
+      - "docs/**"
   release:
     types: [published]
   workflow_dispatch:
@@ -12,7 +14,7 @@ on:
 env:
   NFT_DIFF: "pdiff"
   NFT_DIFF_ARGS: "--line-numbers --width 120 --expand-tabs=2"
-  NFT_VER: "0.9.0"
+  NFT_VER: "0.9.2"
   NFT_WORKDIR: "~"
   NXF_ANSI_LOG: false
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
diff --git a/CHANGELOG.md b/CHANGELOG.md
index bce2ba6729..2b70b0a659 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,10 +5,36 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## dev
+## [3dev](https://github.com/nf-core/sarek/releases/tag/dev) - dev
 
 ### Added
 
+- [1759](https://github.com/nf-core/sarek/pull/1759) - Back to dev
+
+### Changed
+
+### Fixed
+
+### Removed
+
+### Dependencies
+
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+
+### Parameters
+
+| Params | Status |
+| ------ | ------ |
+
+## [3.5.0](https://github.com/nf-core/sarek/releases/tag/3.5.0) - Áhkájiegna
+
+A set of connecting glaciers.
+
+### Added
+
+- [1613](https://github.com/nf-core/sarek/pull/1613) - add indexcov
+- [1638](https://github.com/nf-core/sarek/pull/1638) - Added additional documentation detailing ASCAT WES usage.
 - [1640](https://github.com/nf-core/sarek/pull/1620) - Add `lofreq` as a tumor-only variant caller
 - [1642](https://github.com/nf-core/sarek/pull/1642) - Back to dev
 - [1653](https://github.com/nf-core/sarek/pull/1653) - Updates `sarek_subway` files with `lofreq`
@@ -20,6 +46,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Changed
 
+- [1579](https://github.com/nf-core/sarek/pull/1579) - Update Sentieon usage docs
+- [1635](https://github.com/nf-core/sarek/pull/1635) - Fix docs to reflect variant calling tool - data type correctly
 - [1668](https://github.com/nf-core/sarek/pull/1668) - Add nf-test sharding CI
 - [1669](https://github.com/nf-core/sarek/pull/1669) - Better nf-test pipeline level tests
 - [1677](https://github.com/nf-core/sarek/pull/1677) - Migrate pytest aligner and pipeline default tests to nf-test
@@ -31,6 +59,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [1707](https://github.com/nf-core/sarek/pull/1707) - Un-hide parameters and clean up Json schema
 - [1708](https://github.com/nf-core/sarek/pull/1708) - Migrate pipeline pytest alignment and annotation tests to nf-test
 - [1711](https://github.com/nf-core/sarek/pull/1711) - Migrate pipeline pytest strelka tests to nf-test
+- [1731](https://github.com/nf-core/sarek/pull/1731) - Migrate pipeline pytest controlfreec tests to nf-test
 
 ### Fixed
 
@@ -44,6 +73,12 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [1702](https://github.com/nf-core/sarek/pull/1702) - Update nf-schema tests that were not failing on lenient mode
 - [1712](https://github.com/nf-core/sarek/pull/1712) - Fix missing import statements on error messages when starting without samplesheet
 - [1743](https://github.com/nf-core/sarek/pull/1743) - Add setup java 17 in GHA for latest Nextflow version
+- [1745](https://github.com/nf-core/sarek/pull/1745) - Fix bug where workflow can hang if the email parameter is set
+- [1746](https://github.com/nf-core/sarek/pull/1746) - Fix Sentieon module inputs
+- [1752](https://github.com/nf-core/sarek/pull/1752) - Add `indexcov` and `lofreq` to full size tests. Amend overview figures.
+- [1754](https://github.com/nf-core/sarek/pull/1754) - Fix test string
+- [1755](https://github.com/nf-core/sarek/pull/1755) - Remove `default` channel and name from local modules
+- [1757](https://github.com/nf-core/sarek/pull/1757) - Fix Changelog by adding missing new parameters
 
 ### Removed
 
@@ -59,6 +94,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | `deepvariant` | 1.5.0       | 1.6.1       |
 | `ensemblvep`  | 111.0       | 113.0       |
 | `fgbio`       | 2.0.2       | 2.1.2       |
+| `gawk`        | 5.1.0       | 5.3.0       |
 | `htslib`      | 1.20        | 1.21        |
 | `lofreq`      |             | 2.1.5       |
 | `multiqc`     | 1.21        | 1.25.1      |
@@ -72,6 +108,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | Params                               | Status  |
 | ------------------------------------ | ------- |
 | `--help_full`                        | New     |
+| `--length_required`                  | New     |
 | `--show_hidden`                      | New     |
 | `--snpeff_db`                        | Updated |
 | `--snpeff_genome`                    | Removed |
diff --git a/README.md b/README.md
index 6c501e24c9..fbbe1e5cdd 100644
--- a/README.md
+++ b/README.md
@@ -54,6 +54,7 @@ Depending on the options and samples provided, the pipeline can currently perfor
   - `freebayes`
   - `GATK HaplotypeCaller`
   - `Manta`
+  - `indexcov`
   - `mpileup`
   - `MSIsensor-pro`
   - `Mutect2`
@@ -172,6 +173,7 @@ We thank the following people for their extensive assistance in the development
 - [pallolason](https://github.com/pallolason)
 - [Paul Cantalupo](https://github.com/pcantalupo)
 - [Phil Ewels](https://github.com/ewels)
+- [Pierre Lindenbaum](https://github.com/lindenb)
 - [Sabrina Krakau](https://github.com/skrakau)
 - [Sam Minot](https://github.com/sminot)
 - [Sebastian-D](https://github.com/Sebastian-D)
diff --git a/conf/modules/aligner.config b/conf/modules/aligner.config
index 5f44e199b0..70926d573a 100644
--- a/conf/modules/aligner.config
+++ b/conf/modules/aligner.config
@@ -30,11 +30,11 @@ process {
         }
 
         withName: 'SENTIEON_BWAMEM' {
+            ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.tokenize('.')[0]).concat('.bam') : "${meta.id}.sorted.bam" }
             ext.when   = { params.aligner == 'sentieon-bwamem' }
         }
 
         withName: 'BWAMEM.*_MEM|DRAGMAP_ALIGN|SENTIEON_BWAMEM' {
-            ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.tokenize('.')[0]) : "${meta.id}.sorted" }
             publishDir = [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/preprocessing/" },
@@ -56,6 +56,7 @@ process {
         }
 
         withName: 'BWAMEM.*_MEM|DRAGMAP_ALIGN' {
+            ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.tokenize('.')[0]) : "${meta.id}.sorted" }
             // Markduplicates Spark NEEDS name-sorted reads or runtime goes through the roof
             // However if it's skipped, reads need to be coordinate-sorted
             // Only name sort if Spark for Markduplicates + duplicate marking is not skipped
diff --git a/conf/modules/indexcov.config b/conf/modules/indexcov.config
new file mode 100644
index 0000000000..082ea3b7cc
--- /dev/null
+++ b/conf/modules/indexcov.config
@@ -0,0 +1,21 @@
+
+// INDEXCOV
+
+process {
+    if (params.tools && params.tools.split(',').contains('indexcov')) {
+
+        withName: 'SAMTOOLS_REINDEX_BAM' {
+            ext.args  = { ' -F 3844 -q 30 ' } // high mapq , primary read paired properly mapped
+        }
+
+        withName: 'GOLEFT_INDEXCOV' {
+            publishDir = [
+                mode: params.publish_dir_mode,
+                path: { "${params.outdir}/variant_calling/indexcov/" }
+                ]
+
+        }
+
+    }
+
+}
diff --git a/conf/modules/sentieon_dedup.config b/conf/modules/sentieon_dedup.config
index df52c3bb95..35f89720f7 100644
--- a/conf/modules/sentieon_dedup.config
+++ b/conf/modules/sentieon_dedup.config
@@ -16,7 +16,7 @@
 process {
 
     withName: 'SENTIEON_DEDUP' {
-        ext.prefix       = { "${meta.id}.dedup" }
+        ext.prefix       = { "${meta.id}.dedup.cram" }
         ext.when         = { params.tools && params.tools.split(',').contains('sentieon_dedup') }
         publishDir       = [
             [
diff --git a/conf/test_full.config b/conf/test_full.config
index 8febf40be4..d5bf5d3234 100644
--- a/conf/test_full.config
+++ b/conf/test_full.config
@@ -18,7 +18,7 @@ params {
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/HCC1395_WXS_somatic_full_test.csv'
 
     // Other params
-    tools       = 'ngscheckmate,strelka,mutect2,freebayes,ascat,manta,cnvkit,tiddit,controlfreec,vep,snpeff,muse'
+    tools       = 'ngscheckmate,lofreq,strelka,mutect2,muse,freebayes,ascat,manta,cnvkit,tiddit,controlfreec,vep,snpeff'
     split_fastq = 20000000
     intervals   = 's3://ngi-igenomes/test-data/sarek/S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed'
     wes         = true
diff --git a/conf/test_full_germline.config b/conf/test_full_germline.config
index d731a25709..4b2421c625 100644
--- a/conf/test_full_germline.config
+++ b/conf/test_full_germline.config
@@ -18,6 +18,6 @@ params {
     input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/NA12878_WGS_30x_full_test.csv'
 
     // Other params
-    tools       = 'strelka,freebayes,haplotypecaller,deepvariant,manta,tiddit,cnvkit,vep,snpeff'
+    tools       = 'indexcov,strelka,freebayes,haplotypecaller,deepvariant,manta,tiddit,cnvkit,vep,snpeff'
     split_fastq = 50000000
 }
diff --git a/docs/images/sarek_subway.png b/docs/images/sarek_subway.png
index f2f20ffc01..a381343500 100644
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diff --git a/docs/images/sarek_subway.svg b/docs/images/sarek_subway.svg
index 62544b70fc..6d8d172652 100644
--- a/docs/images/sarek_subway.svg
+++ b/docs/images/sarek_subway.svg
@@ -32,12 +32,12 @@
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        id="tspan23796">freebayes, mutect2, </tspan></tspan><tspan
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+     style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:20px;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro, Normal';font-variant-ligatures:normal;font-variant-caps:normal;font-variant-numeric:normal;font-variant-east-asian:normal;stroke-width:1px"
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        id="tspan23802"
        dx="0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0">   strelka2, lofreq</tspan></tspan><tspan
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+     style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:20px;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro, Normal';font-variant-ligatures:normal;font-variant-caps:normal;font-variant-numeric:normal;font-variant-east-asian:normal;stroke-width:1px"
+     sodipodi:role="line"><tspan
        x="1850.3204"
        y="-1625.3853"
        style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:20px;line-height:1.25;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro, Normal';font-variant-ligatures:normal;font-variant-caps:normal;font-variant-numeric:normal;font-variant-east-asian:normal;stroke-width:1px"
        id="tspan23808"
        dx="0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0">• manta, tiddit</tspan></tspan><tspan
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+     style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:20px;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro, Normal';font-variant-ligatures:normal;font-variant-caps:normal;font-variant-numeric:normal;font-variant-east-asian:normal;stroke-width:1px"
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+     style="font-style:normal;font-variant:normal;font-weight:normal;font-stretch:normal;font-size:20px;font-family:'Maven Pro';-inkscape-font-specification:'Maven Pro, Normal';font-variant-ligatures:normal;font-variant-caps:normal;font-variant-numeric:normal;font-variant-east-asian:normal;stroke-width:1px"
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        id="tspan23820"
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@@ -3374,50 +3380,44 @@
    x="-73.996574"
    y="0"><tspan
      x="21.957031"
-     y="846.21222"
-     id="tspan15">Germline
+     y="845.03542"
+     id="tspan1">Germline
 </tspan><tspan
      x="21.957031"
-     y="877.41223"
-     id="tspan19"><tspan
-       style="font-weight:normal;font-size:26.6667px"
-       id="tspan16">•</tspan><tspan
+     y="876.23543"
+     id="tspan4"><tspan
        style="font-weight:normal;font-size:26.6667px"
-       id="tspan17"> deepvariant, </tspan><tspan
-       style="font-weight:normal;font-size:26.6667px"
-       id="tspan18">freebayes
+       id="tspan3">• deepvariant, freebayes
 </tspan></tspan><tspan
      x="21.957031"
-     y="908.61225"
-     id="tspan22"><tspan
-       style="font-weight:normal;font-size:26.6667px"
-       id="tspan20">   GATK </tspan><tspan
+     y="907.43544"
+     id="tspan6"><tspan
        style="font-weight:normal;font-size:26.6667px"
-       id="tspan21">haplotypecaller,
+       id="tspan5">   GATK haplotypecaller,
 </tspan></tspan><tspan
      x="21.957031"
-     y="939.81226"
-     id="tspan24"><tspan
+     y="938.63545"
+     id="tspan8"><tspan
        style="font-weight:normal;font-size:26.6667px"
-       id="tspan23">   mpileup, strelka2,
+       id="tspan7">   Sentieon haplotyper 
 </tspan></tspan><tspan
      x="21.957031"
-     y="971.01227"
-     id="tspan26"><tspan
+     y="969.83547"
+     id="tspan10"><tspan
        style="font-weight:normal;font-size:26.6667px"
-       id="tspan25">   Sentieon haplotyper
+       id="tspan9">   mpileup, strelka2
 </tspan></tspan><tspan
      x="21.957031"
-     y="1002.2123"
-     id="tspan28"><tspan
+     y="1001.0355"
+     id="tspan12"><tspan
        style="font-weight:normal;font-size:26.6667px"
-       id="tspan27">• manta, tiddit
+       id="tspan11">• indexcov,manta, tiddit
 </tspan></tspan><tspan
      x="21.957031"
-     y="1033.4123"
-     id="tspan34"><tspan
+     y="1032.2355"
+     id="tspan14"><tspan
        style="font-weight:normal;font-size:26.6667px"
-       id="tspan33">• cnvkit</tspan></tspan></text></g><g
+       id="tspan13">• cnvkit</tspan></tspan></text></g><g
    transform="matrix(0.60699338,0,0,-0.60699338,1601.5501,2205.8332)"
    style="display:inline"
    inkscape:label="Sarek"
@@ -3741,7 +3741,11 @@
 
 
 
-</g><style
+<text
+   xml:space="preserve"
+   transform="matrix(0.74999996,0,0,-0.74999996,1552.2133,2357.6141)"
+   id="text2"
+   style="fill:#000000;text-orientation:auto;text-align:start;writing-mode:lr-tb;direction:ltr;font-size:16px;white-space:pre;shape-inside:url(#rect2)" /></g><style
      id="style4691"
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 	.st0{fill:#E01E5A;}
diff --git a/docs/output.md b/docs/output.md
index 048a25b868..b416af724c 100644
--- a/docs/output.md
+++ b/docs/output.md
@@ -46,6 +46,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
     - [Lofreq](#lofreq)
     - [MuSE](#muse)
   - [Structural Variants](#structural-variants)
+    - [Indexcov](#indexcov)
     - [Manta](#manta)
     - [TIDDIT](#tiddit)
   - [Sample heterogeneity, ploidy and CNVs](#sample-heterogeneity-ploidy-and-cnvs)
@@ -607,6 +608,30 @@ For further downstream analysis, take a look [here](https://github.com/Illumina/
 
 ### Structural Variants
 
+#### indexcov
+
+[indexcov](https://github.com/brentp/goleft/tree/master/indexcov) quickly estimate coverage from a whole-genome bam or cram index.
+A bam index has 16KB resolution and it is used as a coverage estimate .
+The output is scaled to around 1. So a long stretch with values of 1.5 would be a heterozygous duplication. This is useful as a quick QC to get coverage values across the genome.
+
+**Output directory: `{outdir}/variantcalling/indexcov/`**
+
+In addition to the interactive HTML files, `indexcov` outputs a number of text files:
+
+- `<sample>-indexcov.ped`: a .ped/.fam file with the inferred sex in the appropriate column if the sex chromosomes were found.
+  the CNX and CNY columns indicating the floating-point estimate of copy-number for those chromosomes.
+  `bins.out`: how many bins had a coverage value outside of (0.85, 1.15). high values can indicate high-bias samples.
+  `bins.lo`: number of bins with value < 0.15. high values indicate missing data.
+  `bins.hi`: number of bins with value > 1.15.
+  `bins.in`: number of bins with value inside of (0.85, 1.15)
+  `p.out`: `bins.out/bins.in`
+  `PC1...PC5`: PCA projections calculated with depth of autosomes.
+
+- `<sample>-indexcov.roc`: tab-delimited columns of chrom, scaled coverage cutoff, and $n_samples columns where each indicates the
+  proportion of 16KB blocks at or above that scaled coverage value.
+- `<sample>-indexcov.bed.gz`: a bed file with columns of chrom, start, end, and a column per sample where the values indicate there
+  scaled coverage for that sample in that 16KB chunk.
+
 #### Manta
 
 [Manta](https://github.com/Illumina/manta) calls structural variants (SVs) and indels from mapped paired-end sequencing reads.
diff --git a/docs/usage.md b/docs/usage.md
index 03a83539db..aa7b1362cc 100644
--- a/docs/usage.md
+++ b/docs/usage.md
@@ -575,22 +575,23 @@ Sarek can be started at different points in the analysis by setting the paramete
 
 This list is by no means exhaustive and it will depend on the specific analysis you would like to run. This is a suggestion based on the individual docs of the tools specifically for human genomes and a garden-variety sequencing run as well as what has been added to the pipeline.
 
-| Tool                                                                                                    | WGS | WES |  Panel |  Normal | Tumor | Somatic |
-| :------------------------------------------------------------------------------------------------------ | :-: | :-: | :----: | :-----: | :---: | :-----: |
-| [DeepVariant](https://github.com/google/deepvariant)                                                    |  x  |  x  |   x    |    x    |   -   |    -    |
-| [FreeBayes](https://github.com/ekg/freebayes)                                                           |  x  |  x  |   x    |    x    |   x   |    x    |
-| [GATK HaplotypeCaller](https://gatk.broadinstitute.org/hc/en-us/articles/5358864757787-HaplotypeCaller) |  x  |  x  |   x    |    x    |   -   |    -    |
-| [GATK Mutect2](https://gatk.broadinstitute.org/hc/en-us/articles/5358911630107-Mutect2)                 |  x  |  x  |   x    |    -    |   x   |    x    |
-| [lofreq](https://github.com/CSB5/lofreq)                                                                |  x  |  x  |   x    |    -    |   x   |    -    |
-| [mpileup](https://www.htslib.org/doc/samtools-mpileup.html)                                             |  x  |  x  |   x    |    x    |   x   |    -    |
-| [Strelka](https://github.com/Illumina/strelka)                                                          |  x  |  x  |   x    |    x    |   -   |    x    |
-| [Manta](https://github.com/Illumina/manta)                                                              |  x  |  x  |   x    |    x    |   x   |    x    |
-| [TIDDIT](https://github.com/SciLifeLab/TIDDIT)                                                          |  x  |  x  |   x    |    x    |   x   |    x    |
-| [ASCAT](https://github.com/VanLoo-lab/ascat)                                                            |  x  |  x  |   -    |    -    |   -   |    x    |
-| [CNVKit](https://cnvkit.readthedocs.io/en/stable/)                                                      |  x  |  x  |   -    |    x    |   x   |    x    |
-| [Control-FREEC](https://github.com/BoevaLab/FREEC)                                                      |  x  |  x  |   x    |    -    |   x   |    x    |
-| [MSIsensorPro](https://github.com/xjtu-omics/msisensor-pro)                                             |  x  |  x  |   x    |    -    |   -   |    x    |
-| [MuSE](https://github.com/wwylab/MuSE)                                                                  |  x  |  x  |   -    |    -    |   -   |    x    |
+| Tool                                                                                                    | WGS | WES |  Panel |  Germline | Tumor-Only | Somatic (Tumor-Normal) |
+| :------------------------------------------------------------------------------------------------------ | :-: | :-: | :----: | :-------: | :--------: | :--------------------: |
+| [DeepVariant](https://github.com/google/deepvariant)                                                    |  x  |  x  |   x    |     x     |     -      |           -            |
+| [FreeBayes](https://github.com/ekg/freebayes)                                                           |  x  |  x  |   x    |     x     |     x      |           x            |
+| [GATK HaplotypeCaller](https://gatk.broadinstitute.org/hc/en-us/articles/5358864757787-HaplotypeCaller) |  x  |  x  |   x    |     x     |     -      |           -            |
+| [GATK Mutect2](https://gatk.broadinstitute.org/hc/en-us/articles/5358911630107-Mutect2)                 |  x  |  x  |   x    |     -     |     x      |           x            |
+| [lofreq](https://github.com/CSB5/lofreq)                                                                |  x  |  x  |   x    |     -     |     x      |           -            |
+| [mpileup](https://www.htslib.org/doc/samtools-mpileup.html)                                             |  x  |  x  |   x    |     x     |     x      |           -            |
+| [Strelka](https://github.com/Illumina/strelka)                                                          |  x  |  x  |   -    |     -     |     -      |           x            |
+| [MuSE](https://github.com/wwylab/MuSE)                                                                  |  x  |  x  |   x    |     -     |     -      |           x            |
+| [Manta](https://github.com/Illumina/manta)                                                              |  x  |  x  |   x    |     x     |     x      |           x            |
+| [indexcov](https://github.com/brentp/goleft/tree/master/indexcov)                                       |  x  |  -  |   -    |     x     |     -      |           x            |
+| [TIDDIT](https://github.com/SciLifeLab/TIDDIT)                                                          |  x  |  x  |   x    |     x     |     x      |           x            |
+| [ASCAT](https://github.com/VanLoo-lab/ascat)                                                            |  x  |  x  |   -    |     -     |     -      |           x            |
+| [CNVKit](https://cnvkit.readthedocs.io/en/stable/)                                                      |  x  |  x  |   -    |     x     |     x      |           x            |
+| [Control-FREEC](https://github.com/BoevaLab/FREEC)                                                      |  x  |  x  |   x    |     -     |     x      |           x            |
+| [MSIsensorPro](https://github.com/xjtu-omics/msisensor-pro)                                             |  x  |  x  |   x    |     -     |     -      |           x            |
 
 ## How to run ASCAT with whole-exome sequencing data?
 
@@ -648,6 +649,89 @@ mv *loci* battenberg_loci_on_target_hg38/
 
 3. Copy the `targets_with_chr.bed` and `GC_G1000_on_target_hg38.txt` files into the newly created `battenberg_loci_on_target_hg38` folder before running the next set of steps. ASCAT generates a list of GC correction loci with sufficient coverage in a sample, then intersects that with the list of all loci with tumour logR values in that sample. If the intersection is <10% the size of the latter, it will fail with an error. Because the Battenberg loci/allele sets are very dense, subsetting to on-target regions is still too many loci. This script ensures that all SNPs with GC correction information are included in the loci list, plus a random sample of another 30% of all on target loci. You may need to vary this proportion depending on your set of targets. A good rule of thumb is that the size of your GC correction loci list should be about 15% the size of your total loci list. This allows for a margin of error.
 
+### 'chr'-based versus non 'chr'-based reference
+
+Please note that loci files provided from ASCAT developers (https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WES) are not 'chr'-based (chromosome names are '1', '2', '3', etc. and not 'chr1', 'chr2', 'chr3', etc.). If your BAMs are 'chr'-based, you will need to add 'chr'
+
+```bash
+for i in {1..22} X;
+  do sed -i 's/^/chr/' G1000_loci_hg19_chr${i}.txt;
+done).
+```
+
+ASCAT will internally remove 'chr' so the other files (allele, GC correction and RT correction) should not be modified and chrom_names (ascat.prepareHTS) should be c(1:22,'X').
+
+If using ASCAT provided references:
+
+```bash
+
+cd .../G1000_lociAll_hg38_unzipped/G1000_lociAll_hg38
+
+# Function to check and correct 'chr' prefix
+check_and_correct_chr_prefix() {
+    local file=$1
+    local chr_number=$2
+
+    # Check if file exists
+    if [ ! -f "$file" ]; then
+        echo "Error: File $file not found."
+        exit 1
+    fi
+
+    # Check first line of the file
+    first_line=$(head -n 1 "$file")
+
+    if [[ $first_line == chr${chr_number}* ]]; then
+        echo "File $file already has correct 'chr' prefix. No changes needed."
+    elif [[ $first_line == chrchr${chr_number}* ]]; then
+        echo "File $file has duplicate 'chr' prefix. Correcting..."
+        sed -i 's/^chrchr/chr/' "$file"
+    elif [[ $first_line == ${chr_number}* ]]; then
+        echo "File $file is missing 'chr' prefix. Adding..."
+        sed -i 's/^/chr/' "$file"
+    else
+        echo "Error: Unexpected format in $file. Please check manually."
+        exit 1
+    fi
+}
+
+# Check and correct 'chr' prefix for each loci file
+for i in {1..22} X; do
+    check_and_correct_chr_prefix "G1000_loci_hg38_chr${i}.txt" "${i}"
+done
+
+for i in {1..22} X
+do
+  # Generate BED file from the tailored loci set
+  awk '{ print $1 "\t" $2-1 "\t" $2 }' G1000_loci_hg38_chr${i}.txt > chr${i}.bed
+
+  # Extract relevant GC content data for this chromosome
+  grep "^chr${i}_" GC_G1000_on_target_hg38.txt > chr${i}.txt
+
+  # Intersect BED file with target regions to find loci on target
+  bedtools intersect -a chr${i}.bed -b targets_with_chr.bed | awk '{ print $1 "_" $3 }' > chr${i}_on_target.txt
+
+  # Calculate the number of lines needed for random sampling (30% of total)
+  n=$(wc -l < chr${i}_on_target.txt)
+  count=$((n * 3 / 10))
+
+  # Get loci that are both on target and match the GC content data
+  grep -xf chr${i}.txt chr${i}_on_target.txt > chr${i}.temp
+
+  # Add random subset of on-target loci to the list
+  shuf -n $count chr${i}_on_target.txt >> chr${i}.temp
+
+  # Sort, remove duplicates, and format output
+  sort -n -k2 -t '_' chr${i}.temp | uniq | awk 'BEGIN { FS="_" } ; { print $1 "\t" $2 }' > battenberg_loci_on_target_hg38_chr${i}.txt
+done
+
+# Compress the resulting loci files into a zip archive
+zip battenberg_loci_on_target_hg38.zip battenberg_loci_on_target_hg38_chr*.txt
+
+```
+
+If using Battenberg provided references:
+
 ```bash
 cd battenberg_loci_on_target_hg38/
 rm *chrstring*
@@ -839,30 +923,30 @@ nextflow run nf-core/sarek --known_indels false --genome GRCh38.GATK
 
 For GATK.GRCh38 the links for each reference file and the corresponding processes that use them is listed below. For GATK.GRCh37 the files originate from the same sources:
 
-| File                  | Tools                                                                                                                                                                                                                                                                                                                                                                                                                                                | Origin                                                                                                                | Docs                                                                                 |
-| :-------------------- | :--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :-------------------------------------------------------------------------------------------------------------------- | :----------------------------------------------------------------------------------- |
-| ascat_alleles         | ASCAT                                                                                                                                                                                                                                                                                                                                                                                                                                                | https://www.dropbox.com/s/uouszfktzgoqfy7/G1000_alleles_hg38.zip                                                      | https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS                   |
-| ascat_loci            | ASCAT                                                                                                                                                                                                                                                                                                                                                                                                                                                | https://www.dropbox.com/s/80cq0qgao8l1inj/G1000_loci_hg38.zip                                                         | https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS                   |
-| ascat_loci_gc         | ASCAT                                                                                                                                                                                                                                                                                                                                                                                                                                                | https://www.dropbox.com/s/80cq0qgao8l1inj/G1000_loci_hg38.zip                                                         | https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS                   |
-| ascat_loci_rt         | ASCAT                                                                                                                                                                                                                                                                                                                                                                                                                                                | https://www.dropbox.com/s/xlp99uneqh6nh6p/RT_G1000_hg38.zip                                                           | https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS                   |
-| bwa                   | bwa-mem                                                                                                                                                                                                                                                                                                                                                                                                                                              | `bwa index -p bwa/${fasta.baseName} $fasta`                                                                           |                                                                                      |
-| bwamem2               | bwa-mem2                                                                                                                                                                                                                                                                                                                                                                                                                                             | `bwa-mem2 index -p bwamem2/${fasta} $fasta`                                                                           |                                                                                      |
-| dragmap               | DragMap                                                                                                                                                                                                                                                                                                                                                                                                                                              | `dragen-os --build-hash-table true --ht-reference $fasta --output-directory dragmap`                                  |                                                                                      |
-| dbsnp                 | Baserecalibrator, ControlFREEC, GenotypeGVCF, HaplotypeCaller                                                                                                                                                                                                                                                                                                                                                                                        | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle       |
-| dbsnp_tbi             | Baserecalibrator, ControlFREEC, GenotypeGVCF, HaplotypeCaller                                                                                                                                                                                                                                                                                                                                                                                        | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) |                                                                                      |
-| dict                  | Baserecalibrator(Spark), CNNScoreVariant, EstimateLibraryComplexity, FilterMutectCalls, FilterVariantTranches, GatherPileupSummaries,GenotypeGVCF, GetPileupSummaries, HaplotypeCaller, MarkDulpicates(Spark), MergeVCFs, Mutect2, Variantrecalibrator                                                                                                                                                                                               | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle       |
-| fasta                 | ApplyBQSR(Spark), ApplyVQSR, ASCAT, Baserecalibrator(Spark), BWA, BWAMem2, CNNScoreVariant, CNVKit, ControlFREEC, DragMap, DEEPVariant, EnsemblVEP, EstimateLibraryComplexity, FilterMutectCalls, FilterVariantTranches, FreeBayes, GatherPileupSummaries,GenotypeGVCF, GetPileupSummaries, HaplotypeCaller, interval building, Manta, MarkDuplicates(Spark),MergeVCFs,MSISensorPro, Mutect2, Samtools, SnpEff, Strelka, Tiddit, Variantrecalibrator | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle       |
-| fasta_fai             | ApplyBQSR(Spark), ApplyVQSR, ASCAT, Baserecalibrator(Spark), BWA, BWAMem2, CNNScoreVariant, CNVKit, ControlFREEC, DragMap, DEEPVariant, EnsemblVEP, EstimateLibraryComplexity, FilterMutectCalls, FilterVariantTranches, FreeBayes, GatherPileupSummaries,GenotypeGVCF, GetPileupSummaries, HaplotypeCaller, interval building, Manta, MarkDuplicates(Spark),MergeVCFs,MSISensorPro, Mutect2, Samtools, SnpEff, Strelka, Tiddit, Variantrecalibrator | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle       |
-| germline_resource     | GetPileupsummaries,Mutect2                                                                                                                                                                                                                                                                                                                                                                                                                           | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) |                                                                                      |
-| germline_resource_tbi | GetPileupsummaries,Mutect2                                                                                                                                                                                                                                                                                                                                                                                                                           | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) |                                                                                      |
-| intervals             | ApplyBQSR(Spark), ASCAT, Baserecalibrator(Spark), BCFTools, CNNScoreVariants, ControlFREEC, Deepvariant, FilterVariantTranches, FreeBayes, GenotypeGVCF, GetPileupSummaries, HaplotypeCaller, Strelka, mpileup, MSISensorPro, Mutect2, VCFTools                                                                                                                                                                                                      | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) |                                                                                      |
-| known_indels          | BaseRecalibrator(Spark), FilterVariantTranches                                                                                                                                                                                                                                                                                                                                                                                                       | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) |                                                                                      |
-| known_indels_tbi      | BaseRecalibrator(Spark), FilterVariantTranches                                                                                                                                                                                                                                                                                                                                                                                                       | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) |                                                                                      |
-| known_snps            | BaseRecalibrator(Spark), FilterVariantTranches, VariantRecalibrator                                                                                                                                                                                                                                                                                                                                                                                  | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) |                                                                                      |
-| known_snps_tbi        | BaseRecalibrator(Spark), FilterVariantTranches, VariantRecalibrator                                                                                                                                                                                                                                                                                                                                                                                  | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) |
-| mappability           | ControlFREEC                                                                                                                                                                                                                                                                                                                                                                                                                                         | http://xfer.curie.fr/get/vyIi4w8EONl/out100m2_hg38.zip                                                                | http://boevalab.inf.ethz.ch/FREEC/tutorial.html                                      |
-| pon                   | Mutect2                                                                                                                                                                                                                                                                                                                                                                                                                                              | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890631-Panel-of-Normals-PON- |
-| pon_tbi               | Mutect2                                                                                                                                                                                                                                                                                                                                                                                                                                              | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890631-Panel-of-Normals-PON- |
+| File                  | Tools                                                                                                                                                                                                                                                                                                                                                                                                                                                          | Origin                                                                                                                | Docs                                                                                 |
+| :-------------------- | :------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | :-------------------------------------------------------------------------------------------------------------------- | :----------------------------------------------------------------------------------- |
+| ascat_alleles         | ASCAT                                                                                                                                                                                                                                                                                                                                                                                                                                                          | https://www.dropbox.com/s/uouszfktzgoqfy7/G1000_alleles_hg38.zip                                                      | https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS                   |
+| ascat_loci            | ASCAT                                                                                                                                                                                                                                                                                                                                                                                                                                                          | https://www.dropbox.com/s/80cq0qgao8l1inj/G1000_loci_hg38.zip                                                         | https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS                   |
+| ascat_loci_gc         | ASCAT                                                                                                                                                                                                                                                                                                                                                                                                                                                          | https://www.dropbox.com/s/80cq0qgao8l1inj/G1000_loci_hg38.zip                                                         | https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS                   |
+| ascat_loci_rt         | ASCAT                                                                                                                                                                                                                                                                                                                                                                                                                                                          | https://www.dropbox.com/s/xlp99uneqh6nh6p/RT_G1000_hg38.zip                                                           | https://github.com/VanLoo-lab/ascat/tree/master/ReferenceFiles/WGS                   |
+| bwa                   | bwa-mem                                                                                                                                                                                                                                                                                                                                                                                                                                                        | `bwa index -p bwa/${fasta.baseName} $fasta`                                                                           |                                                                                      |
+| bwamem2               | bwa-mem2                                                                                                                                                                                                                                                                                                                                                                                                                                                       | `bwa-mem2 index -p bwamem2/${fasta} $fasta`                                                                           |                                                                                      |
+| dragmap               | DragMap                                                                                                                                                                                                                                                                                                                                                                                                                                                        | `dragen-os --build-hash-table true --ht-reference $fasta --output-directory dragmap`                                  |                                                                                      |
+| dbsnp                 | Baserecalibrator, ControlFREEC, GenotypeGVCF, HaplotypeCaller                                                                                                                                                                                                                                                                                                                                                                                                  | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle       |
+| dbsnp_tbi             | Baserecalibrator, ControlFREEC, GenotypeGVCF, HaplotypeCaller                                                                                                                                                                                                                                                                                                                                                                                                  | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) |                                                                                      |
+| dict                  | Baserecalibrator(Spark), CNNScoreVariant, EstimateLibraryComplexity, FilterMutectCalls, FilterVariantTranches, GatherPileupSummaries,GenotypeGVCF, GetPileupSummaries, HaplotypeCaller, MarkDulpicates(Spark), MergeVCFs, Mutect2, Variantrecalibrator                                                                                                                                                                                                         | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle       |
+| fasta                 | ApplyBQSR(Spark), ApplyVQSR, ASCAT, Baserecalibrator(Spark), BWA, BWAMem2, CNNScoreVariant, CNVKit, ControlFREEC, DragMap, DEEPVariant, EnsemblVEP, EstimateLibraryComplexity, FilterMutectCalls, FilterVariantTranches, FreeBayes, GatherPileupSummaries,GenotypeGVCF, GetPileupSummaries, HaplotypeCaller, indexcov, interval building, Manta, MarkDuplicates(Spark),MergeVCFs,MSISensorPro, Mutect2, Samtools, SnpEff, Strelka, Tiddit, Variantrecalibrator | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle       |
+| fasta_fai             | ApplyBQSR(Spark), ApplyVQSR, ASCAT, Baserecalibrator(Spark), BWA, BWAMem2, CNNScoreVariant, CNVKit, ControlFREEC, DragMap, DEEPVariant, EnsemblVEP, EstimateLibraryComplexity, FilterMutectCalls, FilterVariantTranches, FreeBayes, GatherPileupSummaries,GenotypeGVCF, GetPileupSummaries, HaplotypeCaller, indexcov, interval building, Manta, MarkDuplicates(Spark),MergeVCFs,MSISensorPro, Mutect2, Samtools, SnpEff, Strelka, Tiddit, Variantrecalibrator | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890811-Resource-bundle       |
+| germline_resource     | GetPileupsummaries,Mutect2                                                                                                                                                                                                                                                                                                                                                                                                                                     | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) |                                                                                      |
+| germline_resource_tbi | GetPileupsummaries,Mutect2                                                                                                                                                                                                                                                                                                                                                                                                                                     | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) |                                                                                      |
+| intervals             | ApplyBQSR(Spark), ASCAT, Baserecalibrator(Spark), BCFTools, CNNScoreVariants, ControlFREEC, Deepvariant, FilterVariantTranches, FreeBayes, GenotypeGVCF, GetPileupSummaries, HaplotypeCaller, Strelka, mpileup, MSISensorPro, Mutect2, VCFTools                                                                                                                                                                                                                | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) |                                                                                      |
+| known_indels          | BaseRecalibrator(Spark), FilterVariantTranches                                                                                                                                                                                                                                                                                                                                                                                                                 | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) |                                                                                      |
+| known_indels_tbi      | BaseRecalibrator(Spark), FilterVariantTranches                                                                                                                                                                                                                                                                                                                                                                                                                 | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) |                                                                                      |
+| known_snps            | BaseRecalibrator(Spark), FilterVariantTranches, VariantRecalibrator                                                                                                                                                                                                                                                                                                                                                                                            | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) |                                                                                      |
+| known_snps_tbi        | BaseRecalibrator(Spark), FilterVariantTranches, VariantRecalibrator                                                                                                                                                                                                                                                                                                                                                                                            | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) |
+| mappability           | ControlFREEC                                                                                                                                                                                                                                                                                                                                                                                                                                                   | http://xfer.curie.fr/get/vyIi4w8EONl/out100m2_hg38.zip                                                                | http://boevalab.inf.ethz.ch/FREEC/tutorial.html                                      |
+| pon                   | Mutect2                                                                                                                                                                                                                                                                                                                                                                                                                                                        | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890631-Panel-of-Normals-PON- |
+| pon_tbi               | Mutect2                                                                                                                                                                                                                                                                                                                                                                                                                                                        | [GATKBundle](https://console.cloud.google.com/storage/browser/_details/genomics-public-data/resources/broad/hg38/v0/) | https://gatk.broadinstitute.org/hc/en-us/articles/360035890631-Panel-of-Normals-PON- |
 
 ## How to customise SnpEff and VEP annotation
 
@@ -1105,12 +1189,20 @@ Sentieon supply license in the form of a string-value (a url) or a file. It shou
 nextflow secrets set SENTIEON_LICENSE_BASE64 $(echo -n <sentieon_license_string> | base64 -w 0)
 ```
 
+:::note
+<sentieon_license_string> is formatted as `IP:Port` for example: `12.12.12.12:8990`
+:::
+
 If a license file is supplied, then the nextflow secret should be set like this:
 
 ```bash
 nextflow secrets set SENTIEON_LICENSE_BASE64 \$(cat <sentieon_license_file.lic> | base64 -w 0)
 ```
 
+:::note
+If you're looking for documentation on how the nf-core Sentieon GitHub Actions and Sentieon License Server are set up: [Here be dragons.](https://github.com/nf-core/ops/blob/main/pulumi/sentieon_license_server/README.md)
+:::
+
 ### Available Sentieon functions
 
 Sarek contains the following Sentieon functions from [DnaSeq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/) : [bwa mem](https://support.sentieon.com/manual/usages/general/#bwa-mem-syntax), [LocusCollector](https://support.sentieon.com/manual/usages/general/#locuscollector-algorithm) + [Dedup](https://support.sentieon.com/manual/usages/general/#dedup-algorithm), [Haplotyper](https://support.sentieon.com/manual/usages/general/#haplotyper-algorithm), [GVCFtyper](https://support.sentieon.com/manual/usages/general/#gvcftyper-algorithm) and [VarCal](https://support.sentieon.com/manual/usages/general/#varcal-algorithm) + [ApplyVarCal](https://support.sentieon.com/manual/usages/general/#applyvarcal-algorithm), so the basic processing of alignment of fastq-files to VCF-files can be done using speedup Sentieon functions.
@@ -1153,7 +1245,7 @@ Currently, Sentieon's version of BQSR, QualCal, is not available in Sarek. Recen
 ## Requested resources for the tools
 
 Resource requests are difficult to generalize and are often dependent on input data size. Currently, the number of cpus and memory requested by default were adapted from tests on 5 ICGC paired whole-genome sequencing samples with approximately 40X and 80X depth.
-For targeted data analysis, this is overshooting by a lot. In this case resources for each process can be limited by either setting `--max_memory` and `-max_cpus` or tailoring the request by process name as described [here](#resource-requests). If you are using sarek for a certain data type regulary, and would like to make these requests available to others on your system, an institution-specific, pipeline-specific config file can be added [here](https://github.com/nf-core/configs/tree/master/conf/pipeline/sarek).
+For targeted data analysis, this is overshooting by a lot. In this case resources for each process can be limited by tailoring the request by process name as described [here](#resource-requests). If you are using sarek for a certain data type regulary, and would like to make these requests available to others on your system, an institution-specific, pipeline-specific config file can be added [here](https://github.com/nf-core/configs/tree/master/conf/pipeline/sarek).
 
 ## CNV calling with CNVkit
 
diff --git a/docs/usage/variantcalling/sarek.md b/docs/usage/variantcalling/sarek.md
index 150f01d72a..9e071937cd 100644
--- a/docs/usage/variantcalling/sarek.md
+++ b/docs/usage/variantcalling/sarek.md
@@ -88,11 +88,17 @@ They can also be added to the parameters directive in the config file we just ed
 
 ```groovy
 params {
-    max_cpus                  = 2
-    max_memory                = '6.5GB'
-    max_time                  = '2.h'
     use_annotation_cache_keys = true
 }
+
+process {
+    resourceLimits = [
+        cpus: 2,
+        memory: '6.5GB',
+        time: '2.h'
+    ]
+}
+
 ```
 
 The parameter `use_annotation_cache_keys` allows the annotation software to deal with the local paths when the cache is downloaded on the environment.
diff --git a/modules.json b/modules.json
index b774b62291..40fe45721e 100644
--- a/modules.json
+++ b/modules.json
@@ -257,7 +257,8 @@
                     "gatk4/intervallisttobed": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
-                        "installed_by": ["modules"]
+                        "installed_by": ["modules"],
+                        "patch": "modules/nf-core/gatk4/intervallisttobed/gatk4-intervallisttobed.diff"
                     },
                     "gatk4/learnreadorientationmodel": {
                         "branch": "master",
@@ -309,6 +310,11 @@
                         "git_sha": "97321eded31a12598837a476d3615300af413bb7",
                         "installed_by": ["modules"]
                     },
+                    "goleft/indexcov": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "lofreq/callparallel": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
@@ -401,7 +407,7 @@
                     },
                     "samtools/mpileup": {
                         "branch": "master",
-                        "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
+                        "git_sha": "13e7d1046922381df90cd8fe9bee8c3e57ae8457",
                         "installed_by": ["modules"]
                     },
                     "samtools/stats": {
diff --git a/modules/local/add_info_to_vcf/environment.yml b/modules/local/add_info_to_vcf/environment.yml
index 34513c7f4a..315f6dc67e 100644
--- a/modules/local/add_info_to_vcf/environment.yml
+++ b/modules/local/add_info_to_vcf/environment.yml
@@ -1,7 +1,5 @@
-name: gawk
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - anaconda::gawk=5.1.0
+  - conda-forge::gawk=5.3.0
diff --git a/modules/local/create_intervals_bed/environment.yml b/modules/local/create_intervals_bed/environment.yml
index 34513c7f4a..315f6dc67e 100644
--- a/modules/local/create_intervals_bed/environment.yml
+++ b/modules/local/create_intervals_bed/environment.yml
@@ -1,7 +1,5 @@
-name: gawk
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - anaconda::gawk=5.1.0
+  - conda-forge::gawk=5.3.0
diff --git a/modules/local/create_intervals_bed/main.nf b/modules/local/create_intervals_bed/main.nf
index 6a3c9c5a47..ad42e6ad53 100644
--- a/modules/local/create_intervals_bed/main.nf
+++ b/modules/local/create_intervals_bed/main.nf
@@ -72,4 +72,18 @@ process CREATE_INTERVALS_BED {
         END_VERSIONS
         """
     }
+
+    stub:
+    def prefix = task.ext.prefix ?: "${intervals.baseName}"
+    def metrics = task.ext.metrics ?: "${prefix}.metrics"
+    // def prefix_basename = prefix.substring(0, prefix.lastIndexOf("."))
+
+    """
+    touch ${prefix}.stub.bed
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/local/samtools/reindex_bam/environment.yml b/modules/local/samtools/reindex_bam/environment.yml
new file mode 100644
index 0000000000..da2df5e43a
--- /dev/null
+++ b/modules/local/samtools/reindex_bam/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::samtools=1.20
+  - bioconda::htslib=1.20
diff --git a/modules/local/samtools/reindex_bam/main.nf b/modules/local/samtools/reindex_bam/main.nf
new file mode 100644
index 0000000000..153f9093d6
--- /dev/null
+++ b/modules/local/samtools/reindex_bam/main.nf
@@ -0,0 +1,57 @@
+/**
+ * The aim of this process is to re-index the bam file without the duplicate, supplementary, unmapped etc, for goleft/indexcov
+ * It creates a BAM containing only a header (so indexcov can get the sample name) and a BAM index were low quality reads, supplementary etc, have been removed
+ */
+process SAMTOOLS_REINDEX_BAM {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/samtools:1.20--h50ea8bc_0' :
+        'biocontainers/samtools:1.20--h50ea8bc_0' }"
+
+    input:
+    tuple val(meta), path(input), path(input_index)
+    tuple val(meta2), path(fasta)
+    tuple val(meta3), path(fai)
+
+    output:
+    tuple val(meta), path("${meta.id}.reindex.bam"), path("${meta.id}.reindex.bam.bai"),emit: output
+    path  "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def reference = fasta ? "--reference ${fasta}" : ""
+    """
+    # write header only
+    samtools \\
+        view \\
+        --header-only \\
+        --threads ${task.cpus} \\
+        -O BAM \\
+        -o "${meta.id}.reindex.bam" \\
+        ${reference} \\
+        ${input}
+
+    # write BAM index only, remove unmapped, supplementary, etc...
+    samtools \\
+        view \\
+        --uncompressed \\
+        --write-index \\
+        --threads ${task.cpus} \\
+        -O BAM \\
+        -o "/dev/null##idx##${meta.id}.reindex.bam.bai" \\
+        ${reference} \\
+        ${args} \\
+        ${input}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/gatk4/intervallisttobed/gatk4-intervallisttobed.diff b/modules/nf-core/gatk4/intervallisttobed/gatk4-intervallisttobed.diff
new file mode 100644
index 0000000000..03086949c6
--- /dev/null
+++ b/modules/nf-core/gatk4/intervallisttobed/gatk4-intervallisttobed.diff
@@ -0,0 +1,27 @@
+Changes in module 'nf-core/gatk4/intervallisttobed'
+'modules/nf-core/gatk4/intervallisttobed/environment.yml' is unchanged
+'modules/nf-core/gatk4/intervallisttobed/meta.yml' is unchanged
+Changes in 'gatk4/intervallisttobed/main.nf':
+--- modules/nf-core/gatk4/intervallisttobed/main.nf
++++ modules/nf-core/gatk4/intervallisttobed/main.nf
+@@ -40,4 +40,18 @@
+         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
+     END_VERSIONS
+     """
++
++    stub:
++    def prefix = task.ext.prefix ?: "${meta.id}.cram"
++    def metrics = task.ext.metrics ?: "${prefix}.metrics"
++    def prefix_basename = prefix.substring(0, prefix.lastIndexOf("."))
++
++    """
++    touch ${prefix}.bed
++
++    cat <<-END_VERSIONS > versions.yml
++    "${task.process}":
++        gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//')
++    END_VERSIONS
++    """
+ }
+
+************************************************************
diff --git a/modules/nf-core/gatk4/intervallisttobed/main.nf b/modules/nf-core/gatk4/intervallisttobed/main.nf
index 2f6893c0ca..743bb3413a 100644
--- a/modules/nf-core/gatk4/intervallisttobed/main.nf
+++ b/modules/nf-core/gatk4/intervallisttobed/main.nf
@@ -40,4 +40,18 @@ process GATK4_INTERVALLISTTOBED {
         gatk4: \$(echo \$(gatk --version 2>&1) | sed 's/^.*(GATK) v//; s/ .*\$//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}.cram"
+    def metrics = task.ext.metrics ?: "${prefix}.metrics"
+    def prefix_basename = prefix.substring(0, prefix.lastIndexOf("."))
+
+    """
+    touch ${prefix}.bed
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gawk: \$(awk -Wversion | sed '1!d; s/.*Awk //; s/,.*//')
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/goleft/indexcov/environment.yml b/modules/nf-core/goleft/indexcov/environment.yml
new file mode 100644
index 0000000000..813146929c
--- /dev/null
+++ b/modules/nf-core/goleft/indexcov/environment.yml
@@ -0,0 +1,6 @@
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::goleft=0.2.4
+  - bioconda::htslib=1.12
diff --git a/modules/nf-core/goleft/indexcov/main.nf b/modules/nf-core/goleft/indexcov/main.nf
new file mode 100644
index 0000000000..5d0ed5dfb0
--- /dev/null
+++ b/modules/nf-core/goleft/indexcov/main.nf
@@ -0,0 +1,65 @@
+process GOLEFT_INDEXCOV {
+    tag "${meta.id}"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/goleft:0.2.4--h9ee0642_1':
+        'biocontainers/goleft:0.2.4--h9ee0642_1' }"
+
+    input:
+    tuple val(meta), path(bams), path(indexes)
+    tuple val(meta2), path(fai)
+
+    output:
+    tuple val(meta), path("${prefix}/*")          , emit: output
+    tuple val(meta), path("${prefix}/*ped")       , emit: ped , optional: true
+    tuple val(meta), path("${prefix}/*bed.gz")    , emit: bed , optional: true
+    tuple val(meta), path("${prefix}/*bed.gz.tbi"), emit: bed_index , optional: true
+    tuple val(meta), path("${prefix}/*roc")       , emit: roc , optional: true
+    tuple val(meta), path("${prefix}/*html")      , emit: html, optional: true
+    tuple val(meta), path("${prefix}/*png")       , emit: png , optional: true
+    path "versions.yml"                           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    // indexcov uses BAM files or CRAI
+    def input_files = bams.findAll{it.name.endsWith(".bam")} + indexes.findAll{it.name.endsWith(".crai")}
+    def extranormalize = input_files.any{it.name.endsWith(".crai")} ? " --extranormalize " : ""
+    """
+    goleft indexcov \\
+        --fai ${fai}  \\
+        --directory ${prefix} \\
+        ${extranormalize} \\
+        $args \\
+        ${input_files.join(" ")}
+
+    if [ -f "${prefix}/${prefix}-indexcov.bed.gz" ] ; then
+        tabix -p bed "${prefix}/${prefix}-indexcov.bed.gz"
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        goleft: \$(goleft --version 2>&1 | head -n 1 | sed 's/^.*goleft Version: //')
+        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+    END_VERSIONS
+    """
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir "${prefix}"
+    echo "" | gzip > "${prefix}/${prefix}-indexcov.bed.gz"
+    touch "${prefix}/${prefix}-indexcov.bed.gz.tbi"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        goleft: \$(goleft --version 2>&1 | head -n 1 | sed 's/^.*goleft Version: //')
+        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/goleft/indexcov/meta.yml b/modules/nf-core/goleft/indexcov/meta.yml
new file mode 100644
index 0000000000..1619caf32d
--- /dev/null
+++ b/modules/nf-core/goleft/indexcov/meta.yml
@@ -0,0 +1,122 @@
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "goleft_indexcov"
+description: Quickly estimate coverage from a whole-genome bam or cram index. A bam
+  index has 16KB resolution so that's what this gives, but it provides what appears
+  to be a high-quality coverage estimate in seconds per genome.
+keywords:
+  - coverage
+  - cnv
+  - genomics
+  - depth
+tools:
+  - "goleft":
+      description: "goleft is a collection of bioinformatics tools distributed under
+        MIT license in a single static binary"
+      homepage: "https://github.com/brentp/goleft"
+      documentation: "https://github.com/brentp/goleft"
+      tool_dev_url: "https://github.com/brentp/goleft"
+      doi: "10.1093/gigascience/gix090"
+      licence: ["MIT"]
+      identifier: ""
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false]
+    - bams:
+        type: file
+        description: Sorted BAM/CRAM/SAM files
+        pattern: "*.{bam,cram,sam}"
+    - indexes:
+        type: file
+        description: BAI/CRAI files
+        pattern: "*.{bai,crai}"
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false]
+    - fai:
+        type: file
+        description: FASTA index
+        pattern: "*.{fai}"
+output:
+  - output:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/*:
+          type: file
+          description: Files generated by indexcov
+  - ped:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/*ped:
+          type: file
+          description: ped files
+          pattern: "*ped"
+  - bed:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/*bed.gz:
+          type: file
+          description: bed files
+          pattern: "*bed.gz"
+  - bed_index:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/*bed.gz.tbi:
+          type: file
+          description: bed index files
+          pattern: "*bed.gz.tbi"
+  - roc:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/*roc:
+          type: file
+          description: roc files
+          pattern: "*roc"
+  - html:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/*html:
+          type: file
+          description: html files
+          pattern: "*html"
+  - png:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - ${prefix}/*png:
+          type: file
+          description: png files
+          pattern: "*png"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@lindenb"
+maintainers:
+  - "@lindenb"
diff --git a/modules/nf-core/goleft/indexcov/tests/main.nf.test b/modules/nf-core/goleft/indexcov/tests/main.nf.test
new file mode 100644
index 0000000000..1296c644cd
--- /dev/null
+++ b/modules/nf-core/goleft/indexcov/tests/main.nf.test
@@ -0,0 +1,131 @@
+nextflow_process {
+
+    name "Test Process GOLEFT_INDEXCOV"
+    script "../main.nf"
+    process "GOLEFT_INDEXCOV"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "goleft"
+    tag "goleft/indexcov"
+
+    test("sarscov2 - bam") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.sorted.bam", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam", checkIfExists: true)
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.single_end.sorted.bam.bai", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam.bai", checkIfExists: true)
+                    ],
+                ])
+
+                input[1] = Channel.of(
+                    [
+                        [:],
+                        file(params.modules_testdata_base_path + "genomics/sarscov2/genome/genome.fasta.fai", checkIfExists: true)
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.ped,
+                    process.out.bed,
+                    file(process.out.bed_index[0][1]).name,
+                    process.out.roc,
+                    process.out.html,
+                    process.out.png,
+                    process.out.versions
+                    ).match() }
+            )
+        }
+
+    }
+
+
+    test("sarscov2 - crai") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram", checkIfExists: true)
+                    ],
+                    [
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram.crai", checkIfExists: true),
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai", checkIfExists: true)
+                    ]
+                ])
+
+                input[1] = Channel.of(
+                    [
+                        [:],
+                        file(params.modules_testdata_base_path + "genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai", checkIfExists: true)
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.ped,
+                    process.out.bed,
+                    file(process.out.bed_index[0][1]).name,
+                    process.out.roc,
+                    process.out.html,
+                    process.out.png,
+                    process.out.versions
+                    ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test' ], // meta map
+                    [],
+                    []
+                ])
+
+                input[1] = Channel.of([
+                    [:],
+                    []
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/goleft/indexcov/tests/main.nf.test.snap b/modules/nf-core/goleft/indexcov/tests/main.nf.test.snap
new file mode 100644
index 0000000000..1c79232db0
--- /dev/null
+++ b/modules/nf-core/goleft/indexcov/tests/main.nf.test.snap
@@ -0,0 +1,205 @@
+{
+    "sarscov2 - crai": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test-indexcov.ped:md5,8737714b6ea160e06d5282391f89f791"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test-indexcov.bed.gz:md5,04aa3637cffca5d99316df7741c06589"
+                ]
+            ],
+            "test-indexcov.bed.gz.tbi",
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test-indexcov.roc:md5,548b76fdf16e97768b0c9b8ecbfd5bef"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    [
+                        "index.html:md5,41840ede180b20cdf6074c431269929e",
+                        "test-indexcov-depth-chr21.html:md5,4c839b03f2f41e3fdca5642903c35008",
+                        "test-indexcov-roc-chr21.html:md5,f84b547328a23196f16f71d093eb7450"
+                    ]
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    [
+                        "test-indexcov-depth-chr21.png:md5,1999b0bf1cd0680f6d107d438e7257cf",
+                        "test-indexcov-roc-chr21.png:md5,41f1460535b255fff053da59fcccf698"
+                    ]
+                ]
+            ],
+            [
+                "versions.yml:md5,f9c06c1c05a2a31854b4e04e449a24c5"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-22T06:40:17.142801459"
+    },
+    "sarscov2 - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test-indexcov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test-indexcov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test-indexcov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test-indexcov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "4": [
+                    
+                ],
+                "5": [
+                    
+                ],
+                "6": [
+                    
+                ],
+                "7": [
+                    "versions.yml:md5,f9c06c1c05a2a31854b4e04e449a24c5"
+                ],
+                "bed": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test-indexcov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "bed_index": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test-indexcov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "html": [
+                    
+                ],
+                "output": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test-indexcov.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                            "test-indexcov.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        ]
+                    ]
+                ],
+                "ped": [
+                    
+                ],
+                "png": [
+                    
+                ],
+                "roc": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,f9c06c1c05a2a31854b4e04e449a24c5"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-22T06:44:59.203730744"
+    },
+    "sarscov2 - bam": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test-indexcov.ped:md5,da2bd9882474d2f00f8ad2ab20b140c9"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test-indexcov.bed.gz:md5,eab7a78287e261d600c06def12a33029"
+                ]
+            ],
+            "test-indexcov.bed.gz.tbi",
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test-indexcov.roc:md5,3f460308bb86203d1ada71b7c84d995d"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "index.html:md5,d1cc28023cd827446e0f9c905c94fe3e"
+                ]
+            ],
+            [
+                
+            ],
+            [
+                "versions.yml:md5,f9c06c1c05a2a31854b4e04e449a24c5"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-08-22T06:39:48.470187823"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/goleft/indexcov/tests/tags.yml b/modules/nf-core/goleft/indexcov/tests/tags.yml
new file mode 100644
index 0000000000..c27c4b9d5e
--- /dev/null
+++ b/modules/nf-core/goleft/indexcov/tests/tags.yml
@@ -0,0 +1,2 @@
+goleft/indexcov:
+  - "modules/nf-core/goleft/indexcov/**"
diff --git a/modules/nf-core/samtools/mpileup/main.nf b/modules/nf-core/samtools/mpileup/main.nf
index a45c6045b1..925c8244e0 100644
--- a/modules/nf-core/samtools/mpileup/main.nf
+++ b/modules/nf-core/samtools/mpileup/main.nf
@@ -6,13 +6,14 @@ process SAMTOOLS_MPILEUP {
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/samtools:1.21--h50ea8bc_0' :
         'biocontainers/samtools:1.21--h50ea8bc_0' }"
+
     input:
     tuple val(meta), path(input), path(intervals)
     path  fasta
 
     output:
     tuple val(meta), path("*.mpileup.gz"), emit: mpileup
-    path  "versions.yml"                           , emit: versions
+    path  "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -20,15 +21,29 @@ process SAMTOOLS_MPILEUP {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def intervals = intervals ? "-l ${intervals}" : ""
+    def intervals_arg = intervals ? "-l ${intervals}" : ""
     """
     samtools mpileup \\
         --fasta-ref $fasta \\
         --output ${prefix}.mpileup \\
         $args \\
-        $intervals \\
+        $intervals_arg \\
         $input
     bgzip ${prefix}.mpileup
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def intervals_arg = intervals ? "-l ${intervals}" : ""
+    """
+    touch ${prefix}.mpileup.gz
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
diff --git a/nextflow.config b/nextflow.config
index 712167677e..8a00937af5 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -381,7 +381,7 @@ manifest {
     description     = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=24.04.2'
-    version         = '3.5.0dev'
+    version         = '3.6.0dev'
     doi             = '10.12688/f1000research.16665.2, 10.1093/nargab/lqae031, 10.5281/zenodo.3476425'
 }
 
@@ -460,6 +460,7 @@ includeConfig 'conf/modules/controlfreec.config'
 includeConfig 'conf/modules/deepvariant.config'
 includeConfig 'conf/modules/freebayes.config'
 includeConfig 'conf/modules/haplotypecaller.config'
+includeConfig 'conf/modules/indexcov.config'
 includeConfig 'conf/modules/joint_germline.config'
 includeConfig 'conf/modules/manta.config'
 includeConfig 'conf/modules/mpileup.config'
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 61961a3bab..88bc1557d0 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -111,8 +111,8 @@
                     "type": "string",
                     "fa_icon": "fas fa-toolbox",
                     "description": "Tools to use for duplicate marking, variant calling and/or for annotation.",
-                    "help_text": "Multiple tools separated with commas.\n\n**Variant Calling:**\n\nGermline variant calling can currently be performed with the following variant callers:\n- SNPs/Indels: DeepVariant, FreeBayes, GATK HaplotypeCaller, mpileup, Sentieon Haplotyper, Strelka\n- Structural Variants: Manta, TIDDIT\n- Copy-number: CNVKit\n\nTumor-only somatic variant calling can currently be performed with the following variant callers:\n- SNPs/Indels: FreeBayes, mpileup, Mutect2, Lofreq, Strelka\n- Structural Variants: Manta, TIDDIT\n- Copy-number: CNVKit, ControlFREEC\n\nSomatic variant calling can currently only be performed with the following variant callers:\n- SNPs/Indels: FreeBayes, Mutect2, Strelka\n- Structural variants: Manta, TIDDIT\n- Copy-Number: ASCAT, CNVKit, Control-FREEC\n- Microsatellite Instability: MSIsensorpro\n\n> **NB** Mutect2 for somatic variant calling cannot be combined with `--no_intervals`\n\n**Annotation:**\n \n- snpEff, VEP, merge (both consecutively), and bcftools annotate (needs `--bcftools_annotation`).\n\n> **NB** As Sarek will use bgzip and tabix to compress and index VCF files annotated, it expects VCF files to be sorted when starting from `--step annotate`.",
-                    "pattern": "^((ascat|bcfann|cnvkit|controlfreec|deepvariant|freebayes|haplotypecaller|lofreq|sentieon_dnascope|sentieon_haplotyper|manta|merge|mpileup|msisensorpro|mutect2|muse|ngscheckmate|sentieon_dedup|snpeff|strelka|tiddit|vep)?,?)*(?<!,)$"
+                    "help_text": "Multiple tools separated with commas.\n\n**Variant Calling:**\n\nGermline variant calling can currently be performed with the following variant callers:\n- SNPs/Indels: DeepVariant, FreeBayes, GATK HaplotypeCaller, mpileup, Sentieon Haplotyper, Strelka\n- Structural Variants: indexcov, Manta, TIDDIT\n- Copy-number: CNVKit\n\nTumor-only somatic variant calling can currently be performed with the following variant callers:\n- SNPs/Indels: FreeBayes, mpileup, Mutect2, Lofreq, Strelka\n- Structural Variants: Manta, TIDDIT\n- Copy-number: CNVKit, ControlFREEC\n\nSomatic variant calling can currently only be performed with the following variant callers:\n- SNPs/Indels: FreeBayes, Mutect2, Strelka2\n- Structural variants: Manta, TIDDIT\n- Copy-Number: ASCAT, CNVKit, Control-FREEC\n- Microsatellite Instability: MSIsensorpro\n\n> **NB** Mutect2 for somatic variant calling cannot be combined with `--no_intervals`\n\n**Annotation:**\n \n- snpEff, VEP, merge (both consecutively), and bcftools annotate (needs `--bcftools_annotation`).\n\n> **NB** As Sarek will use bgzip and tabix to compress and index VCF files annotated, it expects VCF files to be sorted when starting from `--step annotate`.",
+                    "pattern": "^((ascat|bcfann|cnvkit|controlfreec|deepvariant|muse|freebayes|haplotypecaller|lofreq|sentieon_dnascope|sentieon_haplotyper|manta|indexcov|merge|mpileup|msisensorpro|mutect2|ngscheckmate|sentieon_dedup|snpeff|strelka|tiddit|vep)?,?)*(?<!,)$"
                 },
                 "skip_tools": {
                     "type": "string",
diff --git a/subworkflows/local/bam_joint_calling_germline_sentieon/main.nf b/subworkflows/local/bam_joint_calling_germline_sentieon/main.nf
index 23d0d8675a..0ac47a1e1e 100644
--- a/subworkflows/local/bam_joint_calling_germline_sentieon/main.nf
+++ b/subworkflows/local/bam_joint_calling_germline_sentieon/main.nf
@@ -36,7 +36,7 @@ workflow BAM_JOINT_CALLING_GERMLINE_SENTIEON {
         .map{ meta, gvcf, tbi, intervals -> [ [ id:'joint_variant_calling', intervals_name:intervals.baseName, num_intervals:meta.num_intervals ], gvcf, tbi, intervals ] }
         .groupTuple(by:[0, 3])
 
-    SENTIEON_GVCFTYPER(sentieon_input, fasta.map{meta, it -> [ it ]}, fai.map{meta, it -> [ it ]}, dbsnp, dbsnp_tbi)
+    SENTIEON_GVCFTYPER(sentieon_input, fasta, fai, dbsnp, dbsnp_tbi)
 
     BCFTOOLS_SORT(SENTIEON_GVCFTYPER.out.vcf_gz)
 
diff --git a/subworkflows/local/bam_variant_calling_germline_all/main.nf b/subworkflows/local/bam_variant_calling_germline_all/main.nf
index dfb59cf707..c7666d8fe4 100644
--- a/subworkflows/local/bam_variant_calling_germline_all/main.nf
+++ b/subworkflows/local/bam_variant_calling_germline_all/main.nf
@@ -9,6 +9,7 @@ include { BAM_VARIANT_CALLING_DEEPVARIANT
 include { BAM_VARIANT_CALLING_FREEBAYES                                                } from '../bam_variant_calling_freebayes/main'
 include { BAM_VARIANT_CALLING_GERMLINE_MANTA                                           } from '../bam_variant_calling_germline_manta/main'
 include { BAM_VARIANT_CALLING_HAPLOTYPECALLER                                          } from '../bam_variant_calling_haplotypecaller/main'
+include { BAM_VARIANT_CALLING_INDEXCOV                                                 } from '../bam_variant_calling_indexcov/main'
 include { BAM_VARIANT_CALLING_SENTIEON_DNASCOPE                                        } from '../bam_variant_calling_sentieon_dnascope/main'
 include { BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER                                      } from '../bam_variant_calling_sentieon_haplotyper/main'
 include { BAM_VARIANT_CALLING_MPILEUP                                                  } from '../bam_variant_calling_mpileup/main'
@@ -56,6 +57,7 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
     gvcf_sentieon_dnascope   = Channel.empty()
     gvcf_sentieon_haplotyper = Channel.empty()
 
+    out_indexcov             = Channel.empty()
     vcf_deepvariant          = Channel.empty()
     vcf_freebayes            = Channel.empty()
     vcf_haplotypecaller      = Channel.empty()
@@ -189,6 +191,18 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
         versions = versions.mix(BAM_VARIANT_CALLING_GERMLINE_MANTA.out.versions)
     }
 
+    // INDEXCOV, for WGS only
+    if (params.wes==false &&  tools.split(',').contains('indexcov')) {
+        BAM_VARIANT_CALLING_INDEXCOV (
+            cram,
+            fasta,
+            fasta_fai
+        )
+
+        out_indexcov = BAM_VARIANT_CALLING_INDEXCOV.out.out_indexcov
+        versions = versions.mix(BAM_VARIANT_CALLING_INDEXCOV.out.versions)
+    }
+
     // SENTIEON DNASCOPE
     if (tools.split(',').contains('sentieon_dnascope')) {
         BAM_VARIANT_CALLING_SENTIEON_DNASCOPE(
@@ -354,6 +368,7 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
     emit:
     gvcf_sentieon_dnascope
     gvcf_sentieon_haplotyper
+    out_indexcov
     vcf_all
     vcf_deepvariant
     vcf_freebayes
diff --git a/subworkflows/local/bam_variant_calling_indexcov/main.nf b/subworkflows/local/bam_variant_calling_indexcov/main.nf
new file mode 100644
index 0000000000..d1bc9f39a9
--- /dev/null
+++ b/subworkflows/local/bam_variant_calling_indexcov/main.nf
@@ -0,0 +1,44 @@
+//
+// Indexcov calling
+//
+// For all modules here:
+// A when clause condition is defined in the conf/modules.config to determine if the module should be run
+
+include { SAMTOOLS_REINDEX_BAM } from '../../../modules/local/samtools/reindex_bam/main'
+include { GOLEFT_INDEXCOV      } from '../../../modules/nf-core/goleft/indexcov/main'
+
+// Seems to be the consensus on upstream modules implementation too
+workflow BAM_VARIANT_CALLING_INDEXCOV {
+    take:
+    cram          // channel: [mandatory] [ meta, cram, crai ]
+    fasta         // channel: [mandatory] [ meta, fasta ]
+    fasta_fai     // channel: [mandatory] [ meta, fasta_fai ]
+
+    main:
+    versions = Channel.empty()
+
+    // generate a cleaner bam index without duplicate, supplementary, etc. (Small workload because the bam itself is not re-generated)
+    reindex_ch = SAMTOOLS_REINDEX_BAM(
+        cram,
+        fasta,
+        fasta_fai
+        )
+
+    versions = versions.mix(reindex_ch.versions)
+
+    // create [ [id:directory], bams, bais ]
+    indexcov_input_ch = reindex_ch.output.map{[[id:"indexcov"], it[1], it[2]]}.groupTuple()
+
+    goleft_ch = GOLEFT_INDEXCOV(
+        indexcov_input_ch,
+        fasta_fai
+        )
+
+    versions = versions.mix(goleft_ch.versions)
+
+
+    emit:
+
+    out_indexcov = goleft_ch.output
+    versions
+}
diff --git a/subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf b/subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf
index 1f0d59e522..5c1f1338d2 100644
--- a/subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf
+++ b/subworkflows/local/bam_variant_calling_sentieon_haplotyper/main.nf
@@ -48,9 +48,9 @@ workflow BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER {
     emit_vcf = lst.size() > 0 ? lst[0] : ''
 
     SENTIEON_HAPLOTYPER(
-        cram_intervals_for_sentieon,
-        fasta.map{ meta, it -> it },
-        fasta_fai.map{ meta, it ->  it },
+        cram_intervals_for_sentieon.map{ meta, cram, crai, intervals, num_intervals -> [ meta, cram, crai, intervals, [] ]},
+        fasta,
+        fasta_fai,
         dbsnp,
         dbsnp_tbi,
         emit_vcf,
diff --git a/subworkflows/local/bam_variant_calling_somatic_all/main.nf b/subworkflows/local/bam_variant_calling_somatic_all/main.nf
index f0138c67c5..39e95fca95 100644
--- a/subworkflows/local/bam_variant_calling_somatic_all/main.nf
+++ b/subworkflows/local/bam_variant_calling_somatic_all/main.nf
@@ -13,6 +13,7 @@ include { BAM_VARIANT_CALLING_SOMATIC_MUTECT2           } from '../bam_variant_c
 include { BAM_VARIANT_CALLING_SOMATIC_MUSE              } from '../bam_variant_calling_somatic_muse/main'
 include { BAM_VARIANT_CALLING_SOMATIC_STRELKA           } from '../bam_variant_calling_somatic_strelka/main'
 include { BAM_VARIANT_CALLING_SOMATIC_TIDDIT            } from '../bam_variant_calling_somatic_tiddit/main'
+include { BAM_VARIANT_CALLING_INDEXCOV                  } from '../bam_variant_calling_indexcov/main'
 include { MSISENSORPRO_MSISOMATIC                       } from '../../../modules/nf-core/msisensorpro/msisomatic/main'
 
 workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
@@ -55,6 +56,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
     vcf_mutect2         = Channel.empty()
     vcf_tiddit          = Channel.empty()
     vcf_muse            = Channel.empty()
+    out_indexcov        = Channel.empty()
 
     if (tools.split(',').contains('ascat')) {
         BAM_VARIANT_CALLING_SOMATIC_ASCAT(
@@ -156,6 +158,20 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
         versions = versions.mix(BAM_VARIANT_CALLING_SOMATIC_MANTA.out.versions)
     }
 
+
+    // INDEXCOV, for WGS only
+    if (params.wes==false &&  tools.split(',').contains('indexcov')) {
+        BAM_VARIANT_CALLING_INDEXCOV (
+            cram,
+            fasta,
+            fasta_fai
+        )
+
+        out_indexcov = BAM_VARIANT_CALLING_INDEXCOV.out.out_indexcov
+        versions = versions.mix(BAM_VARIANT_CALLING_INDEXCOV.out.versions)
+    }
+
+
     // STRELKA
     if (tools.split(',').contains('strelka')) {
         // Remap channel to match module/subworkflow
@@ -252,6 +268,7 @@ workflow BAM_VARIANT_CALLING_SOMATIC_ALL {
     )
 
     emit:
+    out_indexcov
     out_msisensorpro
     vcf_all
     vcf_freebayes
diff --git a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf
index f4983278a1..ce568284c7 100644
--- a/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf
+++ b/subworkflows/local/utils_nfcore_sarek_pipeline/main.nf
@@ -183,6 +183,8 @@ workflow PIPELINE_COMPLETION {
     main:
     summary_params = paramsSummaryMap(workflow, parameters_schema: "nextflow_schema.json")
 
+    def multiqc_report_list = multiqc_report.toList()
+
     //
     // Completion email and summary
     //
@@ -195,7 +197,7 @@ workflow PIPELINE_COMPLETION {
                 plaintext_email,
                 outdir,
                 monochrome_logs,
-                multiqc_report.toList()
+                multiqc_report_list.getVal()
             )
         }
 
diff --git a/tests/.nftignore b/tests/.nftignore
index d86cad9bc3..c8aa4b3433 100644
--- a/tests/.nftignore
+++ b/tests/.nftignore
@@ -1,3 +1,4 @@
+.DS_Store
 annotation/**/*.vcf.{gz,gz.tbi}
 csv/*.csv
 multiqc/multiqc_data/gatk-base-recalibrator-reported-empirical-plot.txt
@@ -24,4 +25,4 @@ reports/snpeff/*/*_snpEff.csv
 reports/snpeff/*/snpEff_summary.html
 reports/vcftools/**/*.TsTv.qual
 variant_calling/**/*.vcf.{gz,gz.tbi}
-.DS_Store
+variant_calling/controlfreec/*/config.txt
diff --git a/tests/aligner-bwa-mem.nf.test.snap b/tests/aligner-bwa-mem.nf.test.snap
index c4a5e83995..395ecebba9 100644
--- a/tests/aligner-bwa-mem.nf.test.snap
+++ b/tests/aligner-bwa-mem.nf.test.snap
@@ -17,7 +17,7 @@
                     "samtools": 1.21
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -72,7 +72,7 @@
             5,
             {
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -110,4 +110,4 @@
         },
         "timestamp": "2024-10-08T11:23:05.203586"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/aligner-bwa-mem2.nf.test.snap b/tests/aligner-bwa-mem2.nf.test.snap
index 43d2202bbd..cf062a5aed 100644
--- a/tests/aligner-bwa-mem2.nf.test.snap
+++ b/tests/aligner-bwa-mem2.nf.test.snap
@@ -4,7 +4,7 @@
             5,
             {
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -60,7 +60,7 @@
                     "samtools": 1.21
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -110,4 +110,4 @@
         },
         "timestamp": "2024-10-08T11:25:00.196657"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/aligner-dragmap.nf.test.snap b/tests/aligner-dragmap.nf.test.snap
index 1dd5ce7ded..9cd8406f54 100644
--- a/tests/aligner-dragmap.nf.test.snap
+++ b/tests/aligner-dragmap.nf.test.snap
@@ -4,7 +4,7 @@
             5,
             {
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -64,7 +64,7 @@
                     "samtools": 1.21
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -117,4 +117,4 @@
         },
         "timestamp": "2024-10-08T11:28:12.076906"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/alignment_from_everything.nf.test.snap b/tests/alignment_from_everything.nf.test.snap
index 6ba4bd119b..26c1bf92f2 100644
--- a/tests/alignment_from_everything.nf.test.snap
+++ b/tests/alignment_from_everything.nf.test.snap
@@ -51,7 +51,7 @@
                     "vcftools": "0.1.16"
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -323,7 +323,7 @@
                 "test.strelka.variants.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -332,4 +332,4 @@
         },
         "timestamp": "2024-11-09T21:51:21.998984"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/alignment_to_fastq.nf.test.snap b/tests/alignment_to_fastq.nf.test.snap
index eb7a8ad736..0bf19803d8 100644
--- a/tests/alignment_to_fastq.nf.test.snap
+++ b/tests/alignment_to_fastq.nf.test.snap
@@ -51,7 +51,7 @@
                     "vcftools": "0.1.16"
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -323,7 +323,7 @@
                 "test.strelka.variants.TsTv.count:md5,fa27f678965b7cba6a92efcd039f802a"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -332,4 +332,4 @@
         },
         "timestamp": "2024-11-09T17:49:40.35031"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/annotation_bcfann.nf.test.snap b/tests/annotation_bcfann.nf.test.snap
index 55238c7522..51f7072b12 100644
--- a/tests/annotation_bcfann.nf.test.snap
+++ b/tests/annotation_bcfann.nf.test.snap
@@ -7,7 +7,7 @@
                     "bcftools": 1.2
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -37,4 +37,4 @@
         },
         "timestamp": "2024-10-29T09:38:54.991004"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/annotation_merge.nf.test.snap b/tests/annotation_merge.nf.test.snap
index 4856da93f6..56c6bab95f 100644
--- a/tests/annotation_merge.nf.test.snap
+++ b/tests/annotation_merge.nf.test.snap
@@ -16,7 +16,7 @@
                     "tabix": 1.2
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -122,7 +122,7 @@
                     "tabix": 1.2
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
diff --git a/tests/annotation_snpeff.nf.test.snap b/tests/annotation_snpeff.nf.test.snap
index 012faa171c..a9d51af6ba 100644
--- a/tests/annotation_snpeff.nf.test.snap
+++ b/tests/annotation_snpeff.nf.test.snap
@@ -10,7 +10,7 @@
                     "tabix": 1.2
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -105,4 +105,4 @@
         },
         "timestamp": "2024-10-29T10:16:00.665699"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/annotation_vep.nf.test.snap b/tests/annotation_vep.nf.test.snap
index dd13a715dc..bfbda995eb 100644
--- a/tests/annotation_vep.nf.test.snap
+++ b/tests/annotation_vep.nf.test.snap
@@ -10,7 +10,7 @@
                     "tabix": 1.2
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -280,4 +280,4 @@
         },
         "timestamp": "2024-10-29T10:19:17.846465"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/config/pytesttags.yml b/tests/config/pytesttags.yml
index e86a1c9d7c..0056ace8dd 100644
--- a/tests/config/pytesttags.yml
+++ b/tests/config/pytesttags.yml
@@ -96,27 +96,6 @@ cnvkit:
   - tests/csv/3.0/recalibrated_tumoronly.csv
   - tests/test_cnvkit.yml
 
-## controlfreec
-controlfreec:
-  - conf/modules/controlfreec.config
-  - conf/modules/mpileup.config
-  - modules/nf-core/cat/cat/**
-  - modules/nf-core/controlfreec/assesssignificance/**
-  - modules/nf-core/controlfreec/freec/**
-  - modules/nf-core/controlfreec/freec2bed/**
-  - modules/nf-core/controlfreec/freec2circos/**
-  - modules/nf-core/controlfreec/makegraph2/**
-  - modules/nf-core/mosdepth/**
-  - modules/nf-core/samtools/mpileup/**
-  - subworkflows/local/bam_variant_calling_mpileup/**
-  - subworkflows/local/bam_variant_calling_somatic_all/**
-  - subworkflows/local/bam_variant_calling_somatic_controlfreec/**
-  - subworkflows/local/bam_variant_calling_tumor_only_all/**
-  - subworkflows/local/bam_variant_calling_tumor_only_controlfreec/**
-  - tests/csv/3.0/recalibrated_somatic.csv
-  - tests/csv/3.0/recalibrated_tumoronly.csv
-  - tests/test_controlfreec.yml
-
 ## deepvariant
 deepvariant:
   - conf/modules/deepvariant.config
diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap
index 7cd29cce3c..f6931b8512 100644
--- a/tests/default.nf.test.snap
+++ b/tests/default.nf.test.snap
@@ -39,7 +39,7 @@
                     "vcftools": "0.1.16"
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -322,4 +322,4 @@
         },
         "timestamp": "2024-11-09T21:41:27.897118"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/save_output_as_bam.nf.test.snap b/tests/save_output_as_bam.nf.test.snap
index 665e129414..d2ed3f085d 100644
--- a/tests/save_output_as_bam.nf.test.snap
+++ b/tests/save_output_as_bam.nf.test.snap
@@ -17,7 +17,7 @@
                     "samtools": 1.21
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -33,7 +33,7 @@
                 "reference"
             ],
             [
-                
+
             ],
             [
                 [
@@ -48,4 +48,4 @@
         },
         "timestamp": "2024-10-08T11:11:44.283548"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/saved_mapped.nf.test.snap b/tests/saved_mapped.nf.test.snap
index 13ac090cc8..648822f572 100644
--- a/tests/saved_mapped.nf.test.snap
+++ b/tests/saved_mapped.nf.test.snap
@@ -17,7 +17,7 @@
                     "samtools": 1.21
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -33,10 +33,10 @@
                 "reference"
             ],
             [
-                
+
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -45,4 +45,4 @@
         },
         "timestamp": "2024-10-08T09:53:32.063494"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/sentieon.nf.test b/tests/sentieon.nf.test
new file mode 100644
index 0000000000..2a774e0803
--- /dev/null
+++ b/tests/sentieon.nf.test
@@ -0,0 +1,48 @@
+nextflow_pipeline {
+
+    name "Test sentieon"
+    script "../main.nf"
+    tag "pipeline"
+    tag "pipeline_sarek"
+    tag "sentieon"
+
+    test("stub") {
+
+        tag "stub"
+
+        options "-stub"
+
+        when {
+            params {
+                modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+                outdir = "$outputDir"
+                aligner = "sentieon-bwamem"
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // cram_files: All cram files
+            def cram_files  = getAllFilesFromDir(params.outdir, include: ['**/*.cram'])
+            def fasta       = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta'
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path,
+                    // All cram files
+                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] }
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/tests/sentieon.nf.test.snap b/tests/sentieon.nf.test.snap
new file mode 100644
index 0000000000..5e89a3ae2b
--- /dev/null
+++ b/tests/sentieon.nf.test.snap
@@ -0,0 +1,301 @@
+{
+    "stub": {
+        "content": [
+            23,
+            {
+                "BCFTOOLS_STATS": {
+                    "bcftools": 1.2
+                },
+                "FASTQC": {
+                    "fastqc": "0.12.1"
+                },
+                "GATK4_APPLYBQSR": {
+                    "gatk4": "4.5.0.0"
+                },
+                "GATK4_BASERECALIBRATOR": {
+                    "gatk4": "4.5.0.0"
+                },
+                "GATK4_MARKDUPLICATES": {
+                    "gatk4": "4.5.0.0",
+                    "samtools": "1.19.2"
+                },
+                "INDEX_CRAM": {
+                    "samtools": 1.21
+                },
+                "MOSDEPTH": {
+                    "mosdepth": "0.3.8"
+                },
+                "SAMTOOLS_STATS": {
+                    "samtools": 1.21
+                },
+                "SENTIEON_BWAMEM": {
+                    "sentieon": 202308.03,
+                    "bwa": "0.7.17-r1188"
+                },
+                "STRELKA_SINGLE": {
+                    "strelka": "2.9.10"
+                },
+                "VCFTOOLS_TSTV_COUNT": {
+                    "vcftools": "0.1.16"
+                },
+                "Workflow": {
+                    "nf-core/sarek": "v3.6.0dev"
+                }
+            },
+            [
+                "csv",
+                "csv/markduplicates.csv",
+                "csv/markduplicates_no_table.csv",
+                "csv/recalibrated.csv",
+                "csv/variantcalled.csv",
+                "multiqc",
+                "multiqc/multiqc_data",
+                "multiqc/multiqc_plots",
+                "multiqc/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
+                "preprocessing",
+                "preprocessing/markduplicates",
+                "preprocessing/markduplicates/test",
+                "preprocessing/markduplicates/test/test.cram",
+                "preprocessing/markduplicates/test/test.cram.crai",
+                "preprocessing/recal_table",
+                "preprocessing/recal_table/test",
+                "preprocessing/recal_table/test/test.recal.table",
+                "preprocessing/recalibrated",
+                "preprocessing/recalibrated/test",
+                "preprocessing/recalibrated/test/test.recal.cram",
+                "preprocessing/recalibrated/test/test.recal.cram.crai",
+                "reference",
+                "reports",
+                "reports/bcftools",
+                "reports/bcftools/strelka",
+                "reports/bcftools/strelka/test",
+                "reports/bcftools/strelka/test/test.strelka.variants.bcftools_stats.txt",
+                "reports/fastqc",
+                "reports/fastqc/test-test_L1",
+                "reports/fastqc/test-test_L1/test-test_L1.html",
+                "reports/fastqc/test-test_L1/test-test_L1.zip",
+                "reports/fastqc/test-test_L2",
+                "reports/fastqc/test-test_L2/test-test_L2.html",
+                "reports/fastqc/test-test_L2/test-test_L2.zip",
+                "reports/markduplicates",
+                "reports/markduplicates/test",
+                "reports/markduplicates/test/test.md.cram.metrics",
+                "reports/mosdepth",
+                "reports/mosdepth/test",
+                "reports/mosdepth/test/test.md.global.dist.txt",
+                "reports/mosdepth/test/test.md.per-base.bed.gz",
+                "reports/mosdepth/test/test.md.per-base.bed.gz.csi",
+                "reports/mosdepth/test/test.md.per-base.d4",
+                "reports/mosdepth/test/test.md.quantized.bed.gz",
+                "reports/mosdepth/test/test.md.quantized.bed.gz.csi",
+                "reports/mosdepth/test/test.md.region.dist.txt",
+                "reports/mosdepth/test/test.md.regions.bed.gz",
+                "reports/mosdepth/test/test.md.regions.bed.gz.csi",
+                "reports/mosdepth/test/test.md.summary.txt",
+                "reports/mosdepth/test/test.md.thresholds.bed.gz",
+                "reports/mosdepth/test/test.md.thresholds.bed.gz.csi",
+                "reports/mosdepth/test/test.recal.global.dist.txt",
+                "reports/mosdepth/test/test.recal.per-base.bed.gz",
+                "reports/mosdepth/test/test.recal.per-base.bed.gz.csi",
+                "reports/mosdepth/test/test.recal.per-base.d4",
+                "reports/mosdepth/test/test.recal.quantized.bed.gz",
+                "reports/mosdepth/test/test.recal.quantized.bed.gz.csi",
+                "reports/mosdepth/test/test.recal.region.dist.txt",
+                "reports/mosdepth/test/test.recal.regions.bed.gz",
+                "reports/mosdepth/test/test.recal.regions.bed.gz.csi",
+                "reports/mosdepth/test/test.recal.summary.txt",
+                "reports/mosdepth/test/test.recal.thresholds.bed.gz",
+                "reports/mosdepth/test/test.recal.thresholds.bed.gz.csi",
+                "reports/samtools",
+                "reports/samtools/test",
+                "reports/samtools/test/test.md.cram.stats",
+                "reports/samtools/test/test.recal.cram.stats",
+                "reports/vcftools",
+                "reports/vcftools/strelka",
+                "reports/vcftools/strelka/test",
+                "reports/vcftools/strelka/test/test.strelka.variants.012",
+                "reports/vcftools/strelka/test/test.strelka.variants.012.indv",
+                "reports/vcftools/strelka/test/test.strelka.variants.012.pos",
+                "reports/vcftools/strelka/test/test.strelka.variants.BEAGLE.GL",
+                "reports/vcftools/strelka/test/test.strelka.variants.BEAGLE.PL",
+                "reports/vcftools/strelka/test/test.strelka.variants.FILTER.summary",
+                "reports/vcftools/strelka/test/test.strelka.variants.FORMAT",
+                "reports/vcftools/strelka/test/test.strelka.variants.INFO",
+                "reports/vcftools/strelka/test/test.strelka.variants.LROH",
+                "reports/vcftools/strelka/test/test.strelka.variants.Tajima.D",
+                "reports/vcftools/strelka/test/test.strelka.variants.TsTv",
+                "reports/vcftools/strelka/test/test.strelka.variants.TsTv.count",
+                "reports/vcftools/strelka/test/test.strelka.variants.TsTv.qual",
+                "reports/vcftools/strelka/test/test.strelka.variants.TsTv.summary",
+                "reports/vcftools/strelka/test/test.strelka.variants.bcf",
+                "reports/vcftools/strelka/test/test.strelka.variants.diff.discordance.matrix",
+                "reports/vcftools/strelka/test/test.strelka.variants.diff.indv",
+                "reports/vcftools/strelka/test/test.strelka.variants.diff.indv_in_files",
+                "reports/vcftools/strelka/test/test.strelka.variants.diff.sites",
+                "reports/vcftools/strelka/test/test.strelka.variants.diff.sites_in_files",
+                "reports/vcftools/strelka/test/test.strelka.variants.diff.switch",
+                "reports/vcftools/strelka/test/test.strelka.variants.frq",
+                "reports/vcftools/strelka/test/test.strelka.variants.frq.count",
+                "reports/vcftools/strelka/test/test.strelka.variants.gdepth",
+                "reports/vcftools/strelka/test/test.strelka.variants.geno.chisq",
+                "reports/vcftools/strelka/test/test.strelka.variants.geno.ld",
+                "reports/vcftools/strelka/test/test.strelka.variants.hap.ld",
+                "reports/vcftools/strelka/test/test.strelka.variants.hapcount",
+                "reports/vcftools/strelka/test/test.strelka.variants.het",
+                "reports/vcftools/strelka/test/test.strelka.variants.hwe",
+                "reports/vcftools/strelka/test/test.strelka.variants.idepth",
+                "reports/vcftools/strelka/test/test.strelka.variants.ifreqburden",
+                "reports/vcftools/strelka/test/test.strelka.variants.imiss",
+                "reports/vcftools/strelka/test/test.strelka.variants.impute.hap",
+                "reports/vcftools/strelka/test/test.strelka.variants.impute.hap.indv",
+                "reports/vcftools/strelka/test/test.strelka.variants.impute.hap.legend",
+                "reports/vcftools/strelka/test/test.strelka.variants.indel.hist",
+                "reports/vcftools/strelka/test/test.strelka.variants.interchrom.geno.ld",
+                "reports/vcftools/strelka/test/test.strelka.variants.interchrom.hap.ld",
+                "reports/vcftools/strelka/test/test.strelka.variants.kept.sites",
+                "reports/vcftools/strelka/test/test.strelka.variants.ldepth",
+                "reports/vcftools/strelka/test/test.strelka.variants.ldepth.mean",
+                "reports/vcftools/strelka/test/test.strelka.variants.ldhat.locs",
+                "reports/vcftools/strelka/test/test.strelka.variants.ldhat.sites",
+                "reports/vcftools/strelka/test/test.strelka.variants.list.geno.ld",
+                "reports/vcftools/strelka/test/test.strelka.variants.list.hap.ld",
+                "reports/vcftools/strelka/test/test.strelka.variants.lmiss",
+                "reports/vcftools/strelka/test/test.strelka.variants.lqual",
+                "reports/vcftools/strelka/test/test.strelka.variants.map",
+                "reports/vcftools/strelka/test/test.strelka.variants.mendel",
+                "reports/vcftools/strelka/test/test.strelka.variants.ped",
+                "reports/vcftools/strelka/test/test.strelka.variants.relatedness",
+                "reports/vcftools/strelka/test/test.strelka.variants.relatedness2",
+                "reports/vcftools/strelka/test/test.strelka.variants.removed.sites",
+                "reports/vcftools/strelka/test/test.strelka.variants.singletons",
+                "reports/vcftools/strelka/test/test.strelka.variants.sites.pi",
+                "reports/vcftools/strelka/test/test.strelka.variants.snpden",
+                "reports/vcftools/strelka/test/test.strelka.variants.tfam",
+                "reports/vcftools/strelka/test/test.strelka.variants.tped",
+                "reports/vcftools/strelka/test/test.strelka.variants.vcf",
+                "reports/vcftools/strelka/test/test.strelka.variants.weir.fst",
+                "reports/vcftools/strelka/test/test.strelka.variants.windowed.pi",
+                "variant_calling",
+                "variant_calling/strelka",
+                "variant_calling/strelka/test",
+                "variant_calling/strelka/test/test.strelka.genome.vcf.gz",
+                "variant_calling/strelka/test/test.strelka.genome.vcf.gz.tbi",
+                "variant_calling/strelka/test/test.strelka.variants.vcf.gz",
+                "variant_calling/strelka/test/test.strelka.variants.vcf.gz.tbi"
+            ],
+            [
+                "test.cram:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.cram.crai:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.bcftools_stats.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test-test_L1.html:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test-test_L1.zip:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test-test_L2.html:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test-test_L2.zip:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.md.global.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.md.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "test.md.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.md.per-base.d4:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.md.quantized.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "test.md.quantized.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.md.region.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.md.regions.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "test.md.regions.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.md.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.md.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "test.md.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.recal.global.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.recal.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "test.recal.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.recal.per-base.d4:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.recal.quantized.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "test.recal.quantized.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.recal.region.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.recal.regions.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "test.recal.regions.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "test.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.md.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.012:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.012.indv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.012.pos:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.BEAGLE.GL:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.BEAGLE.PL:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.FILTER.summary:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.FORMAT:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.INFO:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.LROH:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.Tajima.D:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.TsTv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.TsTv.count:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.TsTv.summary:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.bcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.diff.discordance.matrix:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.diff.indv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.diff.indv_in_files:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.diff.sites:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.diff.sites_in_files:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.diff.switch:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.frq:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.frq.count:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.gdepth:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.geno.chisq:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.geno.ld:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.hap.ld:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.hapcount:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.het:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.hwe:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.idepth:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.ifreqburden:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.imiss:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.impute.hap:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.impute.hap.indv:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.impute.hap.legend:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.indel.hist:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.interchrom.geno.ld:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.interchrom.hap.ld:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.kept.sites:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.ldepth:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.ldepth.mean:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.ldhat.locs:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.ldhat.sites:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.list.geno.ld:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.list.hap.ld:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.lmiss:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.lqual:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.map:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.mendel:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.ped:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.relatedness:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.relatedness2:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.removed.sites:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.singletons:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.sites.pi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.snpden:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.tfam:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.tped:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.vcf:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.weir.fst:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "test.strelka.variants.windowed.pi:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+                [
+                    "test.cram",
+                    "d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                [
+                    "test.recal.cram",
+                    "d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-09T10:15:55.105507"
+    }
+}
diff --git a/tests/start_from_markduplicates.nf.test.snap b/tests/start_from_markduplicates.nf.test.snap
index cf769bfcf4..12672ddd02 100644
--- a/tests/start_from_markduplicates.nf.test.snap
+++ b/tests/start_from_markduplicates.nf.test.snap
@@ -16,7 +16,7 @@
                     "samtools": 1.21
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -115,7 +115,7 @@
                 "test.sorted.cram.stats:md5,a15b3a5e59337db312d66020c7bb93ac"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -148,7 +148,7 @@
                     "samtools": 1.21
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -323,7 +323,7 @@
                     "samtools": 1.21
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -475,7 +475,7 @@
                     "samtools": 1.21
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -630,4 +630,4 @@
         },
         "timestamp": "2024-11-09T16:18:25.238396"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/start_from_preparerecalibration.nf.test.snap b/tests/start_from_preparerecalibration.nf.test.snap
index 34bb44c643..485f5ccc37 100644
--- a/tests/start_from_preparerecalibration.nf.test.snap
+++ b/tests/start_from_preparerecalibration.nf.test.snap
@@ -10,7 +10,7 @@
                     "gatk4": "4.5.0.0"
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -55,7 +55,7 @@
                 "multiqc_citations.txt:md5,3815a9f79e41890653a0e0d602c92ac9"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -78,7 +78,7 @@
                     "vcftools": "0.1.16"
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -173,7 +173,7 @@
                 "test.strelka.variants.TsTv.count:md5,ee7dafc8d941b8502a04a63dc3126fff"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -196,7 +196,7 @@
                     "vcftools": "0.1.16"
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -291,7 +291,7 @@
                 "test.strelka.variants.TsTv.count:md5,ee7dafc8d941b8502a04a63dc3126fff"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -314,7 +314,7 @@
                     "samtools": 1.21
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -393,4 +393,4 @@
         },
         "timestamp": "2024-11-09T17:01:30.130705"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/start_from_recalibration.nf.test.snap b/tests/start_from_recalibration.nf.test.snap
index 88a9995819..7347db8471 100644
--- a/tests/start_from_recalibration.nf.test.snap
+++ b/tests/start_from_recalibration.nf.test.snap
@@ -10,7 +10,7 @@
                     "samtools": 1.21
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -80,7 +80,7 @@
                     "vcftools": "0.1.16"
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -175,7 +175,7 @@
                 "test.strelka.variants.TsTv.count:md5,ee7dafc8d941b8502a04a63dc3126fff"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -198,7 +198,7 @@
                     "vcftools": "0.1.16"
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -293,7 +293,7 @@
                 "test.strelka.variants.TsTv.count:md5,ee7dafc8d941b8502a04a63dc3126fff"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -310,7 +310,7 @@
                     "gatk4": "4.5.0.0"
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -332,7 +332,7 @@
                 "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -341,4 +341,4 @@
         },
         "timestamp": "2024-11-09T17:19:08.093003"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/test_controlfreec.yml b/tests/test_controlfreec.yml
deleted file mode 100644
index 5483c69469..0000000000
--- a/tests/test_controlfreec.yml
+++ /dev/null
@@ -1,173 +0,0 @@
-- name: Run variant calling on somatic samples with controlfreec
-  command: nextflow run main.nf -profile test,tools_somatic --tools controlfreec --outdir results
-  tags:
-    - controlfreec
-    - somatic
-    - variant_calling
-    - copy_number_calling
-  files:
-    - path: results/multiqc
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/config.txt
-      contains:
-        [
-          "BedGraphOutput = TRUE",
-          "minExpectedGC = 0",
-          "maxThreads = 2",
-          "noisyData = TRUE",
-          "readCountThreshold = 1",
-          "sex = XX",
-          "window = 10",
-        ]
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.bed
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.circos.txt
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.normal.mpileup.gz_control.cpn
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.p.value.txt
-    # binary changes md5sums on reruns
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_BAF.txt
-    # binary changes md5sums on reruns
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_CNVs
-    # binary changes md5sums on reruns
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_info.txt
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_ratio.BedGraph
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_ratio.txt
-    # binary changes md5sums on reruns
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz_sample.cpn
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_BAF.png
-    # binary changes md5sums on reruns
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.log2.png
-    # binary changes md5sums on reruns
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.png
-    # binary changes md5sums on reruns
-    - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.normal.mpileup.gz
-      should_exist: false
-    - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz
-      should_exist: false
-    - path: results/cnvkit
-      should_exist: false
-    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/sample3/sample3.recal.mosdepth.summary.txt
-    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz
-    - path: results/reports/mosdepth/sample3/sample3.recal.regions.bed.gz.csi
-    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
-    # conda changes md5sums for test
-    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.global.dist.txt
-    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.region.dist.txt
-    - path: results/reports/mosdepth/sample4/sample4.recal.mosdepth.summary.txt
-    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz
-    - path: results/reports/mosdepth/sample4/sample4.recal.regions.bed.gz.csi
-    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
-    # conda changes md5sums for test
-- name: Run variant calling on somatic samples with controlfreec without intervals
-  command: nextflow run main.nf -profile test,tools_somatic --tools controlfreec --no_intervals -stub-run --outdir results
-  tags:
-    - controlfreec
-    - no_intervals
-    - somatic
-    - variant_calling
-    - copy_number_calling
-  files:
-    - path: results/multiqc
-    - path: results/no_intervals.bed
-      md5sum: f3dac01ea66b95fe477446fde2d31489
-    - path: results/no_intervals.bed.gz
-      md5sum: f3dac01ea66b95fe477446fde2d31489
-    - path: results/no_intervals.bed.gz.tbi
-      md5sum: f3dac01ea66b95fe477446fde2d31489
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/GC_profile.sample4_vs_sample3.cpn
-      md5sum: d41d8cd98f00b204e9800998ecf8427e # This is the md5sum of an empty file. Are all these files suppose to be empty?
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/config.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.bed
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.circos.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3.p.value.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_BAF.png
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_BAF.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_CNVs
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_info.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.BedGraph
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.log2.png
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.png
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_ratio.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample4_vs_sample3/sample4_vs_sample3_sample.cpn
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.normal.mpileup.gz
-      should_exist: false
-    - path: results/variant_calling/mpileup/sample4_vs_sample3/sample4_vs_sample3.tumor.mpileup.gz
-      should_exist: false
-    - path: results/controlfreec
-      should_exist: false
-    - path: results/mpileup
-      should_exist: false
-    - path: results/reports/mosdepth/sample3/sample3.recal.global.dist.txt
-    - path: results/reports/mosdepth/sample3/sample3.recal.summary.txt
-    - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz
-    - path: results/reports/mosdepth/sample3/sample3.recal.per-base.bed.gz.csi
-    - path: results/reports/samtools/sample3/sample3.recal.cram.stats
-    # conda changes md5sums for test
-    - path: results/reports/mosdepth/sample4/sample4.recal.global.dist.txt
-    - path: results/reports/mosdepth/sample4/sample4.recal.summary.txt
-    - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz
-    - path: results/reports/mosdepth/sample4/sample4.recal.per-base.bed.gz.csi
-    - path: results/reports/samtools/sample4/sample4.recal.cram.stats
-    # conda changes md5sums for test
-- name: Run variant calling on tumor_only sample with controlfreec
-  command: nextflow run main.nf -profile test,tools_tumoronly --tools controlfreec -stub-run --outdir results
-  tags:
-    - controlfreec
-    - tumor_only
-    - variant_calling
-    - copy_number_calling
-  files:
-    - path: results/multiqc
-    - path: results/variant_calling/controlfreec/sample2/GC_profile.sample2.cpn
-      md5sum: d41d8cd98f00b204e9800998ecf8427e # This is the md5sum of an empty file. Are all these files suppose to be empty?
-    - path: results/variant_calling/controlfreec/sample2/config.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample2/sample2.bed
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample2/sample2.circos.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample2/sample2.p.value.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample2/sample2_BAF.png
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample2/sample2_BAF.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample2/sample2_CNVs
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample2/sample2_info.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample2/sample2_ratio.BedGraph
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample2/sample2_ratio.log2.png
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample2/sample2_ratio.png
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample2/sample2_ratio.txt
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/controlfreec/sample2/sample2_sample.cpn
-      md5sum: d41d8cd98f00b204e9800998ecf8427e
-    - path: results/variant_calling/mpileup/sample2/sample2.tumor.mpileup.gz
-      should_exist: false
-    - path: results/controlfreec
-      should_exist: false
-    - path: results/mpileup
-      should_exist: false
-    - path: results/reports/mosdepth/sample2/sample2.recal.global.dist.txt
-    - path: results/reports/mosdepth/sample2/sample2.recal.region.dist.txt
-    - path: results/reports/mosdepth/sample2/sample2.recal.summary.txt
-    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz
-    - path: results/reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi
-    - path: results/reports/samtools/sample2/sample2.recal.cram.stats
diff --git a/tests/test_fastp.yml b/tests/test_fastp.yml
index 55e714b8c2..3d70bf120d 100644
--- a/tests/test_fastp.yml
+++ b/tests/test_fastp.yml
@@ -78,7 +78,10 @@
     - path: results/reports/fastp/test
     - path: results/reports/fastqc/test-test_L1
     - path: results/reports/markduplicates/test/test.md.cram.metrics
-      contains: ["test	17482	890	170	1047682	12552	69	0	0.65881"]
+      contains:
+        [
+          "LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	SECONDARY_OR_SUPPLEMENTARY_RDS	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE",
+        ]
     - path: results/reports/mosdepth/test/test.md.mosdepth.global.dist.txt
     - path: results/reports/mosdepth/test/test.md.mosdepth.region.dist.txt
     - path: results/reports/mosdepth/test/test.md.mosdepth.summary.txt
diff --git a/tests/test_haplotypecaller.yml b/tests/test_haplotypecaller.yml
index 43cfca38bc..43179e69f0 100644
--- a/tests/test_haplotypecaller.yml
+++ b/tests/test_haplotypecaller.yml
@@ -8,10 +8,6 @@
     - path: results/csv/variantcalled.csv
       md5sum: d7d86e82902a4f57876b2414a4f812a4
     - path: results/multiqc
-    - path: results/preprocessing/converted/test/test.converted.cram
-    # binary changes md5sums on reruns
-    - path: results/preprocessing/converted/test/test.converted.cram.crai
-    # binary changes md5sums on reruns
     - path: results/preprocessing/recalibrated/test/test.recal.cram
       should_exist: false
     - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
@@ -58,10 +54,6 @@
       md5sum: f3dac01ea66b95fe477446fde2d31489
     - path: results/no_intervals.bed.gz.tbi
       md5sum: f3dac01ea66b95fe477446fde2d31489
-    - path: results/preprocessing/converted/test/test.converted.cram
-    # binary changes md5sums on reruns
-    - path: results/preprocessing/converted/test/test.converted.cram.crai
-    # binary changes md5sums on reruns
     - path: results/preprocessing/recalibrated/test/test.recal.cram
       should_exist: false
     - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
diff --git a/tests/test_haplotypecaller_skip_filter.yml b/tests/test_haplotypecaller_skip_filter.yml
index dd9faf7e42..98db41beee 100644
--- a/tests/test_haplotypecaller_skip_filter.yml
+++ b/tests/test_haplotypecaller_skip_filter.yml
@@ -8,10 +8,6 @@
     - path: results/csv/variantcalled.csv
       md5sum: f1041cfc30cedb240f224dd8e3dbf9d2
     - path: results/multiqc
-    - path: results/preprocessing/converted/test/test.converted.cram
-    # binary changes md5sums on reruns
-    - path: results/preprocessing/converted/test/test.converted.cram.crai
-    # binary changes md5sums on reruns
     - path: results/preprocessing/recalibrated/test/test.recal.cram
       should_exist: false
     - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
@@ -61,10 +57,6 @@
       md5sum: f3dac01ea66b95fe477446fde2d31489
     - path: results/no_intervals.bed.gz.tbi
       md5sum: f3dac01ea66b95fe477446fde2d31489
-    - path: results/preprocessing/converted/test/test.converted.cram
-    # binary changes md5sums on reruns
-    - path: results/preprocessing/converted/test/test.converted.cram.crai
-    # binary changes md5sums on reruns
     - path: results/preprocessing/recalibrated/test/test.recal.cram
       should_exist: false
     - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
diff --git a/tests/tumor-normal-pair.nf.test.snap b/tests/tumor-normal-pair.nf.test.snap
index d9d38bee39..e4810e5feb 100644
--- a/tests/tumor-normal-pair.nf.test.snap
+++ b/tests/tumor-normal-pair.nf.test.snap
@@ -42,7 +42,7 @@
                     "vcftools": "0.1.16"
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -390,4 +390,4 @@
         },
         "timestamp": "2024-11-09T18:22:56.125003"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/variant_calling_controlfreec.nf.test b/tests/variant_calling_controlfreec.nf.test
new file mode 100644
index 0000000000..934cf97c4c
--- /dev/null
+++ b/tests/variant_calling_controlfreec.nf.test
@@ -0,0 +1,187 @@
+nextflow_pipeline {
+
+    name "Test pipeline"
+    script "../main.nf"
+    tag "pipeline"
+    tag "pipeline_sarek"
+
+    test("Run with profile test | --tools controlfreec | somatic") {
+
+        when {
+            params {
+                modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+                chr_dir = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz'
+                dbsnp = params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz'
+                dbsnp_tbi = params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi'
+                fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta'
+                fasta_fai = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai'
+                input = "${projectDir}/tests/csv/3.0/recalibrated_somatic.csv"
+                intervals = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed'
+                outdir = "$outputDir"
+                step = "variant_calling"
+                tools = 'controlfreec'
+                wes = true
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // cram_files: All cram files
+            def cram_files  = getAllFilesFromDir(params.outdir, include: ['**/*.cram'])
+            def fasta       = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta'
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path,
+                    // All cram files
+                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] }
+                ).match() }
+            )
+        }
+    }
+
+    test("Run with profile test | --tools controlfreec --no_intervals | tumoronly") {
+
+        when {
+            params {
+                modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+                chr_dir = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz'
+                dbsnp = params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz'
+                dbsnp_tbi = params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi'
+                fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta'
+                fasta_fai = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai'
+                input = "${projectDir}/tests/csv/3.0/recalibrated_tumoronly.csv"
+                no_intervals = true
+                outdir = "$outputDir"
+                step = "variant_calling"
+                tools = 'controlfreec'
+                wes = true
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // cram_files: All cram files
+            def cram_files  = getAllFilesFromDir(params.outdir, include: ['**/*.cram'])
+            def fasta       = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta'
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path,
+                    // All cram files
+                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] }
+                ).match() }
+            )
+        }
+    }
+
+    test("Run with profile test | --tools controlfreec --no_intervals | somatic | stub") {
+        options "-stub"
+        when {
+            params {
+                modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+                chr_dir = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz'
+                dbsnp = params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz'
+                dbsnp_tbi = params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi'
+                fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta'
+                fasta_fai = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai'
+                input = "${projectDir}/tests/csv/3.0/recalibrated_somatic.csv"
+                no_intervals = true
+                outdir = "$outputDir"
+                step = "variant_calling"
+                tools = 'controlfreec'
+                wes = true
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // cram_files: All cram files
+            def cram_files  = getAllFilesFromDir(params.outdir, include: ['**/*.cram'])
+            def fasta       = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta'
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path,
+                    // All cram files
+                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] }
+                ).match() }
+            )
+        }
+    }
+
+    test("Run with profile test | --tools controlfreec | tumoronly | stub") {
+        options "-stub"
+        when {
+            params {
+                modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+                chr_dir = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/chromosomes.tar.gz'
+                dbsnp = params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz'
+                dbsnp_tbi = params.modules_testdata_base_path + '/genomics/homo_sapiens/genome/chr21/germlineresources/dbsnp_138.hg38.vcf.gz.tbi'
+                fasta = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta'
+                fasta_fai = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai'
+                input = "${projectDir}/tests/csv/3.0/recalibrated_tumoronly.csv"
+                intervals = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/chr21/sequence/multi_intervals.bed'
+                outdir = "$outputDir"
+                step = "variant_calling"
+                tools = 'controlfreec'
+                wes = true
+            }
+        }
+
+        then {
+            // stable_name: All files + folders in ${params.outdir}/ with a stable name
+            def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_path: All files in ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // cram_files: All cram files
+            def cram_files  = getAllFilesFromDir(params.outdir, include: ['**/*.cram'])
+            def fasta       = params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta'
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_sarek_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path,
+                    // All cram files
+                    cram_files.collect{ file -> [ file.getName(), cram(file.toString(), fasta).getReadsMD5() ] }
+                ).match() }
+            )
+        }
+    }
+}
diff --git a/tests/variant_calling_controlfreec.nf.test.snap b/tests/variant_calling_controlfreec.nf.test.snap
new file mode 100644
index 0000000000..b4b730687a
--- /dev/null
+++ b/tests/variant_calling_controlfreec.nf.test.snap
@@ -0,0 +1,612 @@
+{
+    "Run with profile test | --tools controlfreec --no_intervals | somatic": {
+        "content": [
+            8,
+            {
+                "SAMTOOLS_MPILEUP": {
+                    "samtools": 1.21
+                },
+                "Workflow": {
+                    "nf-core/sarek": "v3.6.0dev"
+                }
+            },
+            [
+                "csv",
+                "no_intervals.bed",
+                "no_intervals.bed.gz",
+                "no_intervals.bed.gz.tbi",
+                "pipeline_info",
+                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
+                "reference",
+                "reports",
+                "reports/mosdepth",
+                "reports/mosdepth/sample3",
+                "reports/mosdepth/sample3/sample3.recal.mosdepth.global.dist.txt",
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+                "sample4.recal.regions.bed.gz:md5,b7561bc56a955f7db0f11e67e2ec0386",
+                "sample4.recal.regions.bed.gz.csi:md5,538cb5d244411a670a4b041691f8825b",
+                "sample3.recal.cram.stats:md5,bcc229318527e414e69aaa5cd092ad9b",
+                "sample4.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
+                "sample4_vs_sample3.bed:md5,47f60179409e9389e59b2e2525e42210",
+                "sample4_vs_sample3.circos.txt:md5,68addb1d8bda08355842bef0ab15cd6e",
+                "sample4_vs_sample3.normal.mpileup.gz_control.cpn:md5,d50bf2c9a4d35f022364901c284e80ed",
+                "sample4_vs_sample3.p.value.txt:md5,3fad51341e7ee56c3b02de6a51d77efa",
+                "sample4_vs_sample3.tumor.mpileup.gz_BAF.txt:md5,723779bd103b66dcfa6fcfa692135a61",
+                "sample4_vs_sample3.tumor.mpileup.gz_CNVs:md5,1d9166f66bf72adf2aea74adfc4ab015",
+                "sample4_vs_sample3.tumor.mpileup.gz_info.txt:md5,b79da6ae026d86777d60d9f9edb9c6f6",
+                "sample4_vs_sample3.tumor.mpileup.gz_ratio.BedGraph:md5,cb087117ea046a6350885a34cb4bf667",
+                "sample4_vs_sample3.tumor.mpileup.gz_ratio.txt:md5,690cbefd87a77a6a37689135585c401c",
+                "sample4_vs_sample3.tumor.mpileup.gz_sample.cpn:md5,b4f97163fdb6a3d97ca4ea560394cdb1",
+                "sample4_vs_sample3_BAF.png:md5,16456932bb16e79c8cec4f747846c321",
+                "sample4_vs_sample3_ratio.log2.png:md5,89dce170acbb4c438be8359d242940df",
+                "sample4_vs_sample3_ratio.png:md5,6ac35ba93babc019c2d863f7e06b49b1"
+            ],
+            [
+
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-14T16:46:15.872055864"
+    },
+    "Run with profile test | --tools controlfreec | tumoronly | stub": {
+        "content": [
+            13,
+            {
+                "ASSESS_SIGNIFICANCE": {
+                    "controlfreec": 11.6
+                },
+                "FREEC2BED": {
+                    "controlfreec": "11.6b"
+                },
+                "FREEC2CIRCOS": {
+                    "controlfreec": "11.6b"
+                },
+                "FREEC_TUMORONLY": {
+                    "controlfreec": "11.6b"
+                },
+                "MAKEGRAPH2": {
+                    "controlfreec": "11.6b"
+                },
+                "SAMTOOLS_MPILEUP": {
+                    "samtools": 1.21
+                },
+                "Workflow": {
+                    "nf-core/sarek": "v3.6.0dev"
+                }
+            },
+            [
+                "csv",
+                "multiqc",
+                "multiqc/multiqc_data",
+                "multiqc/multiqc_plots",
+                "multiqc/multiqc_report.html",
+                "pipeline_info",
+                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
+                "reference",
+                "reports",
+                "reports/mosdepth",
+                "reports/mosdepth/sample2",
+                "reports/mosdepth/sample2/sample2.recal.global.dist.txt",
+                "reports/mosdepth/sample2/sample2.recal.per-base.bed.gz",
+                "reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi",
+                "reports/mosdepth/sample2/sample2.recal.per-base.d4",
+                "reports/mosdepth/sample2/sample2.recal.quantized.bed.gz",
+                "reports/mosdepth/sample2/sample2.recal.quantized.bed.gz.csi",
+                "reports/mosdepth/sample2/sample2.recal.region.dist.txt",
+                "reports/mosdepth/sample2/sample2.recal.regions.bed.gz",
+                "reports/mosdepth/sample2/sample2.recal.regions.bed.gz.csi",
+                "reports/mosdepth/sample2/sample2.recal.summary.txt",
+                "reports/mosdepth/sample2/sample2.recal.thresholds.bed.gz",
+                "reports/mosdepth/sample2/sample2.recal.thresholds.bed.gz.csi",
+                "reports/samtools",
+                "reports/samtools/sample2",
+                "reports/samtools/sample2/sample2.recal.cram.stats",
+                "variant_calling",
+                "variant_calling/controlfreec",
+                "variant_calling/controlfreec/sample2",
+                "variant_calling/controlfreec/sample2/GC_profile.sample2.cpn",
+                "variant_calling/controlfreec/sample2/config.txt",
+                "variant_calling/controlfreec/sample2/sample2.bed",
+                "variant_calling/controlfreec/sample2/sample2.circos.txt",
+                "variant_calling/controlfreec/sample2/sample2.p.value.txt",
+                "variant_calling/controlfreec/sample2/sample2_BAF.png",
+                "variant_calling/controlfreec/sample2/sample2_BAF.txt",
+                "variant_calling/controlfreec/sample2/sample2_CNVs",
+                "variant_calling/controlfreec/sample2/sample2_info.txt",
+                "variant_calling/controlfreec/sample2/sample2_ratio.BedGraph",
+                "variant_calling/controlfreec/sample2/sample2_ratio.log2.png",
+                "variant_calling/controlfreec/sample2/sample2_ratio.png",
+                "variant_calling/controlfreec/sample2/sample2_ratio.txt",
+                "variant_calling/controlfreec/sample2/sample2_sample.cpn"
+            ],
+            [
+                "sample2.recal.global.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.recal.per-base.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "sample2.recal.per-base.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.recal.per-base.d4:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.recal.quantized.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "sample2.recal.quantized.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.recal.region.dist.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.recal.regions.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "sample2.recal.regions.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.recal.summary.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.recal.thresholds.bed.gz:md5,68b329da9893e34099c7d8ad5cb9c940",
+                "sample2.recal.thresholds.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.recal.cram.stats:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "GC_profile.sample2.cpn:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.bed:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.circos.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2.p.value.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2_BAF.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2_BAF.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2_CNVs:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2_info.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2_ratio.BedGraph:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2_ratio.log2.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2_ratio.png:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2_ratio.txt:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "sample2_sample.cpn:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ],
+            [
+
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-10T10:33:44.36063821"
+    },
+    "Run with profile test | --tools controlfreec --no_intervals | tumoronly": {
+        "content": [
+            11,
+            {
+                "ASSESS_SIGNIFICANCE": {
+                    "controlfreec": 11.6
+                },
+                "FREEC2BED": {
+                    "controlfreec": "11.6b"
+                },
+                "FREEC2CIRCOS": {
+                    "controlfreec": "11.6b"
+                },
+                "FREEC_TUMORONLY": {
+                    "controlfreec": "11.6b"
+                },
+                "MAKEGRAPH2": {
+                    "controlfreec": "11.6b"
+                },
+                "SAMTOOLS_MPILEUP": {
+                    "samtools": 1.21
+                },
+                "Workflow": {
+                    "nf-core/sarek": "v3.6.0dev"
+                }
+            },
+            [
+                "csv",
+                "multiqc",
+                "multiqc/multiqc_data",
+                "multiqc/multiqc_data/multiqc.log",
+                "multiqc/multiqc_data/multiqc_citations.txt",
+                "multiqc/multiqc_data/multiqc_data.json",
+                "multiqc/multiqc_data/multiqc_software_versions.txt",
+                "multiqc/multiqc_data/multiqc_sources.txt",
+                "multiqc/multiqc_report.html",
+                "no_intervals.bed",
+                "no_intervals.bed.gz",
+                "no_intervals.bed.gz.tbi",
+                "pipeline_info",
+                "pipeline_info/nf_core_sarek_software_mqc_versions.yml",
+                "reference",
+                "reports",
+                "reports/mosdepth",
+                "reports/mosdepth/sample2",
+                "reports/mosdepth/sample2/sample2.recal.mosdepth.global.dist.txt",
+                "reports/mosdepth/sample2/sample2.recal.mosdepth.summary.txt",
+                "reports/mosdepth/sample2/sample2.recal.per-base.bed.gz",
+                "reports/mosdepth/sample2/sample2.recal.per-base.bed.gz.csi",
+                "reports/samtools",
+                "reports/samtools/sample2",
+                "reports/samtools/sample2/sample2.recal.cram.stats",
+                "variant_calling",
+                "variant_calling/controlfreec",
+                "variant_calling/controlfreec/sample2",
+                "variant_calling/controlfreec/sample2/config.txt",
+                "variant_calling/controlfreec/sample2/sample2.bed",
+                "variant_calling/controlfreec/sample2/sample2.circos.txt",
+                "variant_calling/controlfreec/sample2/sample2.p.value.txt",
+                "variant_calling/controlfreec/sample2/sample2.tumor.mpileup.gz_BAF.txt",
+                "variant_calling/controlfreec/sample2/sample2.tumor.mpileup.gz_CNVs",
+                "variant_calling/controlfreec/sample2/sample2.tumor.mpileup.gz_info.txt",
+                "variant_calling/controlfreec/sample2/sample2.tumor.mpileup.gz_ratio.BedGraph",
+                "variant_calling/controlfreec/sample2/sample2.tumor.mpileup.gz_ratio.txt",
+                "variant_calling/controlfreec/sample2/sample2.tumor.mpileup.gz_sample.cpn",
+                "variant_calling/controlfreec/sample2/sample2_BAF.png",
+                "variant_calling/controlfreec/sample2/sample2_ratio.log2.png",
+                "variant_calling/controlfreec/sample2/sample2_ratio.png"
+            ],
+            [
+                "multiqc_citations.txt:md5,4c806e63a283ec1b7e78cdae3a923d4f",
+                "sample2.recal.mosdepth.global.dist.txt:md5,f2dcd00a64947c49e8e4b93c2f4fbf27",
+                "sample2.recal.mosdepth.summary.txt:md5,0a7300e56eda6fba7c7564f00aa000f0",
+                "sample2.recal.per-base.bed.gz:md5,39a1bc436aa8546c26faedbe94cb676c",
+                "sample2.recal.per-base.bed.gz.csi:md5,aaa7bed9e7ef873b23bca249b8b58eb9",
+                "sample2.recal.cram.stats:md5,0d1784cb4c3f14b9858247ac6128dd03",
+                "sample2.bed:md5,5249f46e614b60867bdd6b9b83327979",
+                "sample2.circos.txt:md5,2efab24d023931cec8b158c56d1f1765",
+                "sample2.p.value.txt:md5,38c8c9ad33a4fca3804a34d5c436cd1e",
+                "sample2.tumor.mpileup.gz_BAF.txt:md5,0bb91da6a637ed64d7622eb7d539fd71",
+                "sample2.tumor.mpileup.gz_CNVs:md5,741831784091e9a51e0c07117b67e18f",
+                "sample2.tumor.mpileup.gz_info.txt:md5,fed6aa0e0f4232255d5152f5774161b9",
+                "sample2.tumor.mpileup.gz_ratio.BedGraph:md5,d2347daecbb4eb1f1a3b5558acdf657a",
+                "sample2.tumor.mpileup.gz_ratio.txt:md5,7587b17b4303715aa45eae017e357c23",
+                "sample2.tumor.mpileup.gz_sample.cpn:md5,8bf25e5cf94e89bcbbd4bb0d453d3057",
+                "sample2_BAF.png:md5,32e1189f07f9ddb4892cae10f4003e4a",
+                "sample2_ratio.log2.png:md5,6d8b8cabc35d391f9a92ede6128eb378",
+                "sample2_ratio.png:md5,47fce58116c63d6cad34f80575e34e43"
+            ],
+            [
+
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-14T16:47:40.762784422"
+    }
+}
diff --git a/tests/variant_calling_strelka.nf.test.snap b/tests/variant_calling_strelka.nf.test.snap
index bf8ed3bc8d..a2c281a07f 100644
--- a/tests/variant_calling_strelka.nf.test.snap
+++ b/tests/variant_calling_strelka.nf.test.snap
@@ -16,7 +16,7 @@
                     "vcftools": "0.1.16"
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -195,7 +195,7 @@
                 "sample4_vs_sample3.strelka.somatic_snvs.TsTv.count:md5,fc7af1f534890c4ad3025588b3af62ae"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -221,7 +221,7 @@
                     "vcftools": "0.1.16"
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -375,7 +375,7 @@
                 "sample4_vs_sample3.strelka.somatic_snvs.TsTv.count:md5,a922c51ca3b2ea7cdcfa09e9c8c55d52"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -401,7 +401,7 @@
                     "vcftools": "0.1.16"
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -552,7 +552,7 @@
                 "sample4_vs_sample3.strelka.somatic_snvs.TsTv.count:md5,fc7af1f534890c4ad3025588b3af62ae"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -575,7 +575,7 @@
                     "vcftools": "0.1.16"
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -686,7 +686,7 @@
                 "sample1.strelka.variants.TsTv.count:md5,c5b7a8eda2526d899098439ae4c06a49"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -709,7 +709,7 @@
                     "vcftools": "0.1.16"
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -823,7 +823,7 @@
                 "sample1.strelka.variants.TsTv.count:md5,1481854d2a765f5641856ecf95ca4097"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -832,4 +832,4 @@
         },
         "timestamp": "2024-11-15T22:25:42.940353635"
     }
-}
\ No newline at end of file
+}
diff --git a/tests/variant_calling_strelka_bp.nf.test.snap b/tests/variant_calling_strelka_bp.nf.test.snap
index 1ab795aa31..c0398176b3 100644
--- a/tests/variant_calling_strelka_bp.nf.test.snap
+++ b/tests/variant_calling_strelka_bp.nf.test.snap
@@ -22,7 +22,7 @@
                     "vcftools": "0.1.16"
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -212,7 +212,7 @@
                 "sample4_vs_sample3.strelka.somatic_snvs.TsTv.count:md5,a922c51ca3b2ea7cdcfa09e9c8c55d52"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -244,7 +244,7 @@
                     "vcftools": "0.1.16"
                 },
                 "Workflow": {
-                    "nf-core/sarek": "v3.5.0dev"
+                    "nf-core/sarek": "v3.6.0dev"
                 }
             },
             [
@@ -431,7 +431,7 @@
                 "sample4_vs_sample3.strelka.somatic_snvs.TsTv.count:md5,fc7af1f534890c4ad3025588b3af62ae"
             ],
             [
-                
+
             ]
         ],
         "meta": {
@@ -440,4 +440,4 @@
         },
         "timestamp": "2024-11-15T22:37:23.231917992"
     }
-}
\ No newline at end of file
+}
diff --git a/workflows/sarek/main.nf b/workflows/sarek/main.nf
index 7595c279e7..f554cd9ddd 100644
--- a/workflows/sarek/main.nf
+++ b/workflows/sarek/main.nf
@@ -16,6 +16,7 @@ include { CHANNEL_BASERECALIBRATOR_CREATE_CSV               } from '../../subwor
 include { CHANNEL_APPLYBQSR_CREATE_CSV                      } from '../../subworkflows/local/channel_applybqsr_create_csv/main'
 include { CHANNEL_VARIANT_CALLING_CREATE_CSV                } from '../../subworkflows/local/channel_variant_calling_create_csv/main'
 
+
 // Convert BAM files to FASTQ files
 include { BAM_CONVERT_SAMTOOLS as CONVERT_FASTQ_INPUT       } from '../../subworkflows/local/bam_convert_samtools/main'
 include { BAM_CONVERT_SAMTOOLS as CONVERT_FASTQ_UMI         } from '../../subworkflows/local/bam_convert_samtools/main'
@@ -609,6 +610,7 @@ workflow SAREK {
         }
     }
 
+
     if (params.step == 'variant_calling') {
 
         cram_variant_calling = Channel.empty().mix( input_sample )
@@ -799,6 +801,8 @@ workflow SAREK {
         reports = reports.mix(VCF_QC_BCFTOOLS_VCFTOOLS.out.vcftools_tstv_counts.collect{ meta, counts -> [ counts ] })
         reports = reports.mix(VCF_QC_BCFTOOLS_VCFTOOLS.out.vcftools_tstv_qual.collect{ meta, qual -> [ qual ] })
         reports = reports.mix(VCF_QC_BCFTOOLS_VCFTOOLS.out.vcftools_filter_summary.collect{ meta, summary -> [ summary ] })
+        reports = reports.mix(BAM_VARIANT_CALLING_GERMLINE_ALL.out.out_indexcov.collect{ meta, indexcov -> indexcov.flatten() })
+        reports = reports.mix(BAM_VARIANT_CALLING_SOMATIC_ALL.out.out_indexcov.collect{ meta, indexcov -> indexcov.flatten() })
 
         CHANNEL_VARIANT_CALLING_CREATE_CSV(vcf_to_annotate, params.outdir)