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nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://nf-co.re/sarek
MIT License
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mixing tumor-only and paired samples and having a tool that only works for paired samples causes the pipeline to fail #948

Closed FriederikeHanssen closed 2 months ago

FriederikeHanssen commented 1 year ago

Description of the bug

When specifying mixed samples (tumor-only and paired) and some tools do not work for tumor-only, like msisensorpro, the pipeline will fail.

Reported by @MolPath-Bioinfo on Slack https://nfcore.slack.com/archives/CGFUX04HZ/p1676972372078189?thread_ts=1676897338.792179&cid=CGFUX04HZ

I am guessing we went a bit overboard with validating the tools parameter on input sample sheet parsing.

Command used and terminal output

No response

Relevant files

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System information

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FriederikeHanssen commented 1 year ago

hm I can't reproduce this issue. Tested with nextflow run main.nf -profile test,variantcalling_channels,docker --tools msisensorpro --outdir ./results the samplesheet contains:

patient,sex,status,sample,cram,crai
test,XX,0,sample1,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai
test1,XX,1,sample2,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai
test3,XX,0,sample3,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai
test3,XX,1,sample4,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram,https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai

So a mix of paired and tumor-only sample. Using msisensorpro I would expect a failure based on the report, but it works fine for me.

FriederikeHanssen commented 1 year ago

I will need more info on the issue to fix.

MolPath-Bioinfo commented 1 year ago

Hi. I will try another mixed run this week and get back to you.

Von: Friederike Hanssen @.***> Gesendet: Montag, 29. Mai 2023 12:31:02 An: nf-core/sarek Cc: Mihaela Martis-Thiele; Mention Betreff: Re: [nf-core/sarek] mixing tumor-only and paired samples and having a tool that only works for paired samples causes the pipeline to fail (Issue #948)

I will need more info on the issue to fix.

— Reply to this email directly, view it on GitHubhttps://github.com/nf-core/sarek/issues/948#issuecomment-1566935800, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AWZR5QSQWURALA7UYUXM23DXIR3GNANCNFSM6AAAAAAVC2A4IQ. You are receiving this because you were mentioned.Message ID: @.***>

FriederikeHanssen commented 2 months ago

closed as non reproducable. Please reopen if you encounter this issue again