Merge branch 'dev' into muse

nf-core · Jan 7, 2025 · c4b2725 · c4b2725
2 parents 59dde7b + e4c7791
commit c4b2725
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diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -5,14 +5,16 @@ on:
     branches:
       - dev
   pull_request:
+    paths-ignore:
+      - "docs/**"
   release:
     types: [published]
   workflow_dispatch:
 
 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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