The sample-sheet only contains tumor-samples #1260

bounlu · 2023-09-29T08:08:02Z

Description of the bug

I am getting a new type of error when running the same sample samplesheet as it used to work before:

The sample-sheet only contains tumor-samples, but the following tools, which were requested by the option "tools", expect at least one normal-sample : ascat, msisensorpro
Files within --vep_cache invalid. Make sure there is a directory named homo_sapiens/110_GRCh38 in s3://annotation-cache/vep_cache/.
https://nf-co.re/sarek/dev/usage#how-to-customise-snpeff-and-vep-annotation
The sample-sheet only contains normal-samples, but the following tools, which were requested with "--tools", expect at least one tumor-sample : ascat, controlfreec, mutect2, msisensorpro

The sample sheet contains both normal and tumor samples though.

Command used and terminal output

nextflow run nf-core/sarek \
-latest \
-profile docker \
--step mapping \
--tools freebayes,mpileup,mutect2,strelka,manta,tiddit,ascat,cnvkit,controlfreec,msisensorpro,snpeff,vep,merge \
--input 'samplesheet_sarek.csv' \
--outdir '/nextflow/sarek/results/' \
-work-dir '/nextflow/sarek/work/' \
-c 'custom.config' \
-r master \
-resume

Relevant files

No response

System information

N E X T F L O W ~ version 23.08.1-edge
local
Docker
Linux
nf-core/sarek master v3.3.1

The text was updated successfully, but these errors were encountered:

maxulysse · 2023-09-29T09:12:04Z

Can you share the .nextflow.log?

bounlu · 2023-10-02T01:36:32Z

Here you go:

nextflow.log

asp8200 · 2023-10-02T06:38:53Z

I guess it would also be relevant for us to inspect the sample sheet. Can you also share that with us?

maxulysse · 2023-10-02T08:33:15Z

Yeah, I think the issue is unrelated to that error.
Can you try the same command and add --use_annotation_cache_keys?

acpicornell · 2023-10-02T11:51:06Z

Same error here using nextflow-23.04.4-all
--use_annotation_cache_keys makes no difference.
I am using normal samples (marked as 0 in the samplesheet) and I get:

The sample-sheet only contains tumor-samples, but the following tools, which were requested by the option "tools", expect at least one normal-sample : deepvariant, haplotypecaller
Process 'CNNSCOREVARIANTS' has been already used -- If you need to reuse the same component, include it with a different name or include it in a different workflow context

maxulysse · 2023-10-02T14:47:01Z

Can you share the log file please?

berguner · 2023-10-03T15:24:11Z

I am also getting the same error even though my sample sheet contains only normal samples (0), not tumor samples.

maxulysse · 2023-10-03T15:39:56Z

can you share the log file?

berguner · 2023-10-03T16:07:28Z

I also got the Files within --vep_cache invalid error and I fixed it by providing the VEP cache files for Ensembl 110. Strangely, this also fixed the The sample-sheet only contains tumor-samples error.

maxulysse · 2023-10-03T16:11:09Z

@bounlu Can you try without snpeff,vep,merge to see if I can rule out my hypothesis?

maxulysse · 2023-10-03T16:11:41Z

I also got the Files within --vep_cache invalid error and I fixed it by providing the VEP cache files for Ensembl 110. Strangely, this also fixed the The sample-sheet only contains tumor-samples error.

Yeah, I think the 2 are fully unrelated, but no idea why the The sample-sheet only contains tumor-samples gets triggered.

bounlu · 2023-10-03T16:20:40Z

Without snpeff,vep,merge I also don't get error.

acpicornell · 2023-10-04T06:54:59Z

Can you share the log file please?

nextflow.log

this is my "launcher":

export JAVA_HOME="/home/acpicornell/.sdkman/candidates/java/17.0.6-amzn"
export NXF_VER=23.04.4
/mnt/storage/$(whoami)/bin/nextflow run /mnt/storage/$(whoami)/pipelines/nf-core-sarek_3.3.1/3_3_1/\
     --max_memory       100.0GB\
     --max_cpus         32\
     --input            /mnt/storage/$(whoami)/nfcore/sarek/230908/samplesheet.csv\
     --outdir           /mnt/storage/$(whoami)/nfcore/sarek/230908/output\
     --step             mapping\
     --genome           GATK.GRCh38\
     --igenomes_base    /mnt/storage/$(whoami)/references\
     --tools            deepvariant,freebayes,haplotypecaller,mpileup,strelka,sentieon_haplotyper\
     --aligner          bwa-mem2\
     --seq_platform     ILLUMINA\
     --wes              false\
     -profile           singularity\

All my samples are germline and I am not annotating. This is what I get:

Process 'CNNSCOREVARIANTS' has been already used -- If you need to reuse the same component, include it with a different name or include it in a different workflow context

 -- Check script '/mnt/storage/acpicornell/pipelines/nf-core-sarek_3.3.1/3_3_1/./workflows/../subworkflows/local/bam_variant_calling_germline_all/../vcf_variant_filtering_gatk/main.nf' at line: 22 or see '.nextflow.log' file for more details
The sample-sheet only contains tumor-samples, but the following tools, which were requested by the option "tools", expect at least one normal-sample : deepvariant, haplotypecaller

maxulysse · 2023-10-04T08:45:39Z

ok, so https://github.com/nf-core/sarek/releases/tag/3.3.2 should fix these issues

bounlu · 2023-10-04T14:06:17Z

I still get similar error with the new version:

The sample-sheet only contains normal-samples, but the following tools, which were requested with "--tools", expect at least one tumor-sample : ascat, controlfreec, mutect2, msisensorpro
Files within --vep_cache invalid. Make sure there is a directory named homo_sapiens/110_GRCh38 in s3://annotation-cache/vep_cache/.
https://nf-co.re/sarek/usage#how-to-customise-snpeff-and-vep-annotation
The sample-sheet only contains tumor-samples, but the following tools, which were requested by the option "tools", expect at least one normal-sample : ascat, msisensorpro

maxulysse · 2023-10-04T14:14:23Z

ok, so we get all error messages at once, but I think it all lies with this error:

Files within --vep_cache invalid. Make sure there is a directory named homo_sapiens/110_GRCh38 in s3://annotation-cache/vep_cache/.
https://nf-co.re/sarek/usage#how-to-customise-snpeff-and-vep-annotation

maxulysse · 2023-10-04T14:27:27Z

in your case @bounlu I'd say that adding --use_annotation_cache_keys or using a local cache should solve your issue

sisterdot · 2023-10-22T14:19:47Z

hey!

also got the error

Files within --vep_cache invalid. Make sure there is a directory named homo_sapiens/110_GRCh38 in s3://annotation-cache/vep_cache/.
https://nf-co.re/sarek/usage#how-to-customise-snpeff-and-vep-annotation
The sample-sheet only contains tumor-samples, but the following tools, which were requested by the option "tools", expect at least one normal-sample : deepvariant, haplotypecaller

when starting

nextflow run  nf-core/sarek -r 3.3.2  --outdir results_sarek_3.3.2  --input parameter.csv --genome GATK.GRCh38 --tools cnvkit,deepvariant,freebayes,haplotypecaller,manta,mpileup,snpeff,vep,strelka,tiddit,merge

in my understanding the error is linked to the check in
if (params.vep_cache == "s3://annotation-cache/vep_cache") {
which evaluates to false in my test case

as does
if (params.snpeff_cache == "s3://annotation-cache/snpeff_cache") {

if i explicitly define the parameters (before tools) when starting the pipeline both comparisons will actually evaluate to true and no confusing error is raised (should be the same value as default, but maybe different type, a groovy expert might know):

nextflow run  nf-core/sarek -r 3.3.2 --snpeff_cache s3://annotation-cache/snpeff_cache --vep_cache s3://annotation-cache/vep_cache --outdir results_sarek_3.3.2  --input parameter.csv --genome GATK.GRCh38 --tools cnvkit,deepvariant,freebayes,haplotypecaller,manta,mpileup,snpeff,vep,strelka,tiddit,merge

  nf-core/sarek v3.3.2-gf034b73
  containerEngine           : singularity
  nextflow version 23.04.2.5871
  CentOS Linux release 7.9.2009

achakroun · 2023-11-06T18:18:37Z

Hello,
It seems to be a conflict with "--tools" setting. I had the following (same) error with nf-core/sarek v3.3.2-gf034b73:

The sample-sheet only contains tumor-samples, but the following tools, which were requested by the option "tools", expect at least one normal-sample : deepvariant, haplotypecaller Process 'CNNSCOREVARIANTS' has been already used -- If you need to reuse the same component, include it with a different name or include it in a different workflow context

and it worked fine for me when I set:

--tools deepvariant,freebayes,sentieon_haplotyper,strelka,manta,tiddit,cnvkit

or

--tools deepvariant,haplotypecaller,freebayes,strelka,manta,tiddit,cnvkit

instead of:

--tools deepvariant,freebayes,haplotypecaller,sentieon_haplotyper,strelka,manta,tiddit,cnvkit

FriederikeHanssen · 2023-11-07T08:34:31Z

@achakroun can you send everything you used? Samplesheet, full command, the .nextflow.log, any custom configuration files?

achakroun · 2023-11-07T08:41:12Z

@achakroun can you send everything you used? Samplesheet, full command, the .nextflow.log, any custom configuration files?

Sure

1- Command:

nextflow run nf-core/sarek -profile singularity -resume --max_cpus 10 --max_memory 40.GB --input ./samplesheet.csv --trim_fastq --genome GATK.GRCh38 --save_reference --outdir ./results --wes --intervals Twist_Exome_RefSeq_targets_hg38_200-pad.bed --tools deepvariant,haplotypecaller,freebayes,strelka,manta,tiddit,cnvkit --concatenate_vcfs

2- Samplesheet was like:

patient,status,sample,lane,fastq_1,fastq_2 841-23,0,841-23,Lane2,fastq/841-23_1.fastq.gz,fastq/841-23_2.fastq.gz 842-23,0,842-23,Lane2,fastq/842-23_1.fastq.gz,fastq/842-23_2.fastq.gz

Nothing else.

FriederikeHanssen · 2023-11-07T08:42:27Z

can you send the .nextflow.logfile as well

achakroun · 2023-11-07T08:46:29Z

Please, note that the pipe is still running
.nextflow.log

FriederikeHanssen · 2023-11-07T09:53:42Z

Sorry can you provide the log from the failed run?

FriederikeHanssen · 2023-11-07T09:56:37Z

ah pretty sure I know what is wrong. opened a separate issue to fix --> #1314

sfilges · 2023-11-07T13:24:03Z

hey!

also got the error
Files within --vep_cache invalid. Make sure there is a directory named homo_sapiens/110_GRCh38 in s3://annotation-cache/vep_cache/.
https://nf-co.re/sarek/usage#how-to-customise-snpeff-and-vep-annotation
The sample-sheet only contains tumor-samples, but the following tools, which were requested by the option "tools", expect at least one normal-sample : deepvariant, haplotypecaller
when starting
nextflow run  nf-core/sarek -r 3.3.2  --outdir results_sarek_3.3.2  --input parameter.csv --genome GATK.GRCh38 --tools cnvkit,deepvariant,freebayes,haplotypecaller,manta,mpileup,snpeff,vep,strelka,tiddit,merge 
in my understanding the error is linked to the check in if (params.vep_cache == "s3://annotation-cache/vep_cache") { which evaluates to false in my test case

as does if (params.snpeff_cache == "s3://annotation-cache/snpeff_cache") {

if i explicitly define the parameters (before tools) when starting the pipeline both comparisons will actually evaluate to true and no confusing error is raised (should be the same value as default, but maybe different type, a groovy expert might know):
nextflow run  nf-core/sarek -r 3.3.2 --snpeff_cache s3://annotation-cache/snpeff_cache --vep_cache s3://annotation-cache/vep_cache --outdir results_sarek_3.3.2  --input parameter.csv --genome GATK.GRCh38 --tools cnvkit,deepvariant,freebayes,haplotypecaller,manta,mpileup,snpeff,vep,strelka,tiddit,merge
  nf-core/sarek v3.3.2-gf034b73
  containerEngine           : singularity
  nextflow version 23.04.2.5871
  CentOS Linux release 7.9.2009

this fixed the error for me.

FriederikeHanssen · 2023-11-07T13:57:13Z

Hey! Yeah those are two completely unrelated issues, just nf-validation both times bubbles up The sample-sheet only contains tumor-samples, but the following tools, which were requested by the option "tools", expect at least one normal-sample : deepvariant, haplotypecaller this for some reason. But the real hint is in the other half of the error message

FriederikeHanssen · 2023-11-07T19:23:40Z

@achakroun your issue is fixed on dev

charlesdavid · 2024-06-15T02:35:41Z

Hey, this problem has not been entirely fixed...
I am running with a local genome with ignore igenomes set and have a sample sheet with both status entered: 0 and 1.
However, this error is still occurring making the workflow un-runnable for version: nf-core/sarek v3.4.2

nextflow.exception.WorkflowScriptErrorException: The sample-sheet only contains tumor-samples, but the following tools, which were requested by the option "tools", expect at least one normal-sample : haplotypecaller

COMMAND:

nextflow \ main.nf \ -c "pfr_profile.config" \ -profile pfr,singularity \ -params-file "pfr_params.json" \ --input ${INPUT} \ --outdir "${OUT_DIR}" \ --genome null \ --igenomes_ignore \ --wes true \ --skip_tools baserecalibrator \ --tools "freebayes,haplotypecaller,mpileup" \ --fasta ${FASTA} \ --fasta_fai ${FAI} \ --dict ${DICT} \ --trim_fastq true \ --save_trimmed true \ --save_reference \ --save_mapped true \ --save_output_as_bam true \ -resume

Note, the pfr profile only specifies SLURM as the executor.

pfr_params.jason:

{ "genome": null, "igenomes_ignore": true, "save_reference": true, "split_fastq": 50000000, "trim_fastq": true, "save_trimmed": true, "aligner": "bwa-mem", "save_mapped": true, "save_output_as_bam": true }

Here is the error in the log file:

Jun-14 23:58:10.815 [main] DEBUG nextflow.executor.ExecutorFactory - << taskConfig executor: slurm Jun-14 23:58:10.815 [main] DEBUG nextflow.executor.ExecutorFactory - >> processorType: 'slurm' Jun-14 23:58:10.831 [main] DEBUG nextflow.Session - Config process names validation disabled as requested Jun-14 23:58:10.833 [main] DEBUG nextflow.Session - Igniting dataflow network (184) Jun-14 23:58:10.844 [Actor Thread 5] ERROR nextflow.extension.OperatorImpl - @unknown java.lang.NullPointerException: Cannot get property 'baseName' on null object at org.codehaus.groovy.runtime.NullObject.getProperty(NullObject.java:60) at org.codehaus.groovy.runtime.InvokerHelper.getProperty(InvokerHelper.java:190) at org.codehaus.groovy.runtime.callsite.NullCallSite.getProperty(NullCallSite.java:46) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.callGetProperty(AbstractCallSite.java:329) at Script_48a2d276$_runScript_closure1$_closure2$_closure6.doCall(Script_48a2d276:132) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:568) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035) at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:38) at org.codehaus.groovy.runtime.callsite.CallSiteArray.defaultCall(CallSiteArray.java:47) at org.codehaus.groovy.runtime.callsite.PogoMetaClassSite.call(PogoMetaClassSite.java:53) at org.codehaus.groovy.runtime.callsite.AbstractCallSite.call(AbstractCallSite.java:139) at nextflow.extension.MapOp$_apply_closure1.doCall(MapOp.groovy:56) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:568) at org.codehaus.groovy.reflection.CachedMethod.invoke(CachedMethod.java:107) at groovy.lang.MetaMethod.doMethodInvoke(MetaMethod.java:323) at org.codehaus.groovy.runtime.metaclass.ClosureMetaClass.invokeMethod(ClosureMetaClass.java:274) at groovy.lang.MetaClassImpl.invokeMethod(MetaClassImpl.java:1035) at groovy.lang.Closure.call(Closure.java:412) at groovyx.gpars.dataflow.operator.DataflowOperatorActor.startTask(DataflowOperatorActor.java:120) at groovyx.gpars.dataflow.operator.DataflowOperatorActor.onMessage(DataflowOperatorActor.java:108) at groovyx.gpars.actor.impl.SDAClosure$1.call(SDAClosure.java:43) at groovyx.gpars.actor.AbstractLoopingActor.runEnhancedWithoutRepliesOnMessages(AbstractLoopingActor.java:293) at groovyx.gpars.actor.AbstractLoopingActor.access$400(AbstractLoopingActor.java:30) at groovyx.gpars.actor.AbstractLoopingActor$1.handleMessage(AbstractLoopingActor.java:93) at groovyx.gpars.util.AsyncMessagingCore.run(AsyncMessagingCore.java:132) at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136) at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635) at java.base/java.lang.Thread.run(Thread.java:833)

Here is the sample sheet:

`
patient,status,sample,lane,fastq_1,fastq_2

GC,1,GC_CAT13ANXX_TTAGGC,L001,/WGS/AGRF_CAGRF14129_CAT13ANXX/DH_A_GC_CAT13ANXX_TTAGGC_L001_R1.fastq.gz,/WGS/AGRF_CAGRF14129_CAT13ANXX/DH_A_GC_CAT13ANXX_TTAGGC_L001_R2.fastq.gz
GC,1,GC_CAT13ANXX_TTAGGC,L002,/WGS/AGRF_CAGRF14129_CAT13ANXX/DH_A_GC_CAT13ANXX_TTAGGC_L002_R1.fastq.gz,/WGS/AGRF_CAGRF14129_CAT13ANXX/DH_A_GC_CAT13ANXX_TTAGGC_L002_R2.fastq.gz
GC,1,GC_CAT13ANXX_TTAGGC,L003,/WGS/AGRF_CAGRF14129_CAT13ANXX/DH_A_GC_CAT13ANXX_TTAGGC_L003_R1.fastq.gz,/WGS/AGRF_CAGRF14129_CAT13ANXX/DH_A_GC_CAT13ANXX_TTAGGC_L003_R2.fastq.gz
SW,0,SW_CAT13ANXX_TGACCA,L001,/WGS/AGRF_CAGRF14129_CAT13ANXX/DH_B_SW_CAT13ANXX_TGACCA_L001_R1.fastq.gz,/WGS/AGRF_CAGRF14129_CAT13ANXX/DH_B_SW_CAT13ANXX_TGACCA_L001_R2.fastq.gz
SW,0,SW_CAT13ANXX_TGACCA,L002,/WGS/AGRF_CAGRF14129_CAT13ANXX/DH_B_SW_CAT13ANXX_TGACCA_L002_R1.fastq.gz,/WGS/AGRF_CAGRF14129_CAT13ANXX/DH_B_SW_CAT13ANXX_TGACCA_L002_R2.fastq.gz
SW,0,SW_CAT13ANXX_TGACCA,L003,/WGS/AGRF_CAGRF14129_CAT13ANXX/DH_B_SW_CAT13ANXX_TGACCA_L003_R1.fastq.gz,/WGS/AGRF_CAGRF14129_CAT13ANXX/DH_B_SW_CAT13ANXX_TGACCA_L003_R2.fastq.gz
`

maxulysse · 2024-06-17T10:14:10Z

@charlesdavid can you send the file for the samplesheet?

kenibrewer · 2024-06-17T13:45:49Z

@charlesdavid
Your sample sheet appears to have "two" patients. One with the id GC that is all tumor samples and other named SW that is all normal. The tools that you're trying to run requires samples to have the same patient id with at least some tumor and some normal.

@maxulysse It might be good to close this issue as the most recent comments are helping troubleshoot user issues. Leaving it in the open state makes it seem that there is still something that needs to be fixed with sarek. Perhaps it would be good to improve the clarity of that error message though as it still seems to cause confusion.

maxulysse · 2024-06-17T17:19:14Z

This issue has been fixed, @charlesdavid your issue is now #1567.
Thanks @kenibrewer for the idea

bounlu · 2024-08-13T07:11:44Z

This bug emerged again after the latest merging of the dev version into master 3.4.3. This time it says sample-sheet only contains normal-samples:

The sample-sheet only contains normal-samples, but the following tools, which were requested with "--tools", expect at least one tumor-sample : controlfreec, mutect2
Missing process or function Channel.empty([[]])

 -- Check script '/home/omeran/.nextflow/assets/nf-core/sarek/main.nf' at line: 342 or see '.nextflow.log' file for more details

This was a resume from a previous successful run with the same command line. It worked then and now it fails again.

FriederikeHanssen · 2024-08-13T07:20:13Z

I am guessing false flag from the error message (it for some reason shows up for unrelated issues). What is in the .nextflow.log & samplesheet

bounlu · 2024-08-13T07:26:39Z

What should be the correct format of the full path to the caches? There is also discrepancy between the documentation help text and the actual cache files located on igenomes S3:

https://nf-co.re/sarek/3.4.3/parameters/#vep_cache says:
${vep_species}/${vep_genome}_${vep_cache_version}

S3 has:
s3://annotation-cache/vep_cache/111_GRCh38/homo_sapiens/111_GRCh38/

I am using a local cache and it seems I need to update the path format to make it work with the 3.4.3.

asp8200 · 2024-08-13T10:34:07Z

I think I also encountered that problem. Fixed it locally with some symlinks.

bounlu · 2024-08-14T02:36:00Z

@asp8200

Can you please share your directory tree for the cache dirs?

asp8200 · 2024-08-14T10:37:39Z

We already had vep_cache/110_GRCh38/homo_sapiens/110_GRCh38 downloaded from previous (old) versions of Sarek, and I had to introduce a symlink from vep_cache/homo_sapiens/110_GRCh38 to vep_cache/110_GRCh38/homo_sapiens/110_GRCh38 for Sarek v3.4.2. (I haven't tried with Sarek v3.4.3 yet.)

I suspect that @maxulysse changed the folder structure for the vep-cache (and snpeff-cache), but perhaps he can comment on that?

Dorothynyamai · 2025-01-10T17:08:50Z

Hi @maxulysse & @FriederikeHanssen,

Thank you for your support on nf-core. I am still getting the "The sample-sheet only contains normal-samples, but the following tools, which were requested with "--tools", expect at least one tumor-sample : mutect2" error even though my samplesheet has tumor-normal pairs. I have attached the sample file and nextflow.log file. i used the commands:
nextflow
run ./sarek/3.4.4/nf-core-sarek_3.4.4/3_4_4
-profile singularity
--aligner bwa-mem2
--save_mapped
-c ./sarek_offline.config
--input ./paired_files.csv
--outdir ./sarek_results
-w ./temp_output
--genome GATK.GRCh38
--igenomes_base ./nf-core_igenomes_references
--wes
--intervals ./target_sorted_unique.bed
--tools manta,strelka,freebayes,tiddit,cnvkit,mutect2,deepvariant
-offline

nextflow.log

sample_sheet.csv

FriederikeHanssen · 2025-01-10T17:51:29Z

There is a compatibility bug with that version of nextflow and sarek 3.4.4 can you either downgrade nextflow to 24.04 or upgrade sarek?

bounlu added the bug Something isn't working label Sep 29, 2023

FriederikeHanssen mentioned this issue Nov 7, 2023

When both sentieon_haplotype and haplotypecaller are provided, config scopes are clashing #1314

Closed

maxulysse mentioned this issue Jun 17, 2024

samplesheet issue #1567

Closed

maxulysse closed this as completed Jun 17, 2024

asp8200 mentioned this issue Aug 14, 2024

Misleading info on Documentation #1621

Closed

ashpsnair mentioned this issue Nov 25, 2024

The sample-sheet only contains normal-samples error #1740

Open

The sample-sheet only contains tumor-samples #1260

The sample-sheet only contains tumor-samples #1260

Comments

bounlu commented Sep 29, 2023

Description of the bug

Command used and terminal output

Relevant files

System information

maxulysse commented Sep 29, 2023

bounlu commented Oct 2, 2023

asp8200 commented Oct 2, 2023

maxulysse commented Oct 2, 2023

acpicornell commented Oct 2, 2023

maxulysse commented Oct 2, 2023

berguner commented Oct 3, 2023

maxulysse commented Oct 3, 2023

berguner commented Oct 3, 2023

maxulysse commented Oct 3, 2023

maxulysse commented Oct 3, 2023

bounlu commented Oct 3, 2023

acpicornell commented Oct 4, 2023 • edited Loading

maxulysse commented Oct 4, 2023

bounlu commented Oct 4, 2023

maxulysse commented Oct 4, 2023

maxulysse commented Oct 4, 2023

sisterdot commented Oct 22, 2023

achakroun commented Nov 6, 2023 • edited Loading

FriederikeHanssen commented Nov 7, 2023

achakroun commented Nov 7, 2023 • edited Loading

FriederikeHanssen commented Nov 7, 2023

achakroun commented Nov 7, 2023

FriederikeHanssen commented Nov 7, 2023

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acpicornell commented Oct 4, 2023 •

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achakroun commented Nov 6, 2023 •

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achakroun commented Nov 7, 2023 •

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