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Tiddit for tumor varcalling#597

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FriederikeHanssen merged 11 commits intonf-core:devfrom
WackerO:tiddit
Jun 23, 2022
Merged

Tiddit for tumor varcalling#597
FriederikeHanssen merged 11 commits intonf-core:devfrom
WackerO:tiddit

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@WackerO WackerO commented Jun 20, 2022 •
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This PR adds tiddit for tumor variant calling analogous to #581.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
    • If you've added a new tool - add to the software_versions process and a regex to scrape_software_versions.py
    • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
    • If necessary, also make a PR on the nf-core/sarek branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint .).
  • Ensure the test suite passes (nextflow run . -profile test,docker).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

@WackerO WackerO requested a review from maxulysse as a code owner June 20, 2022 06:17
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github-actions Bot commented Jun 20, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 656af02

+| ✅ 145 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-06-23 11:25:54

maxulysse
maxulysse reviewed Jun 20, 2022
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Comment thread subworkflows/local/pair_variant_calling.nf Outdated
@WackerO WackerO changed the title Tiddit for pair and tumor varcalling Tiddit for tumor varcalling Jun 22, 2022
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WackerO commented Jun 22, 2022

Just removed pair VC, will look at that separately so that tumor tiddit can be merged already. Note: I checked the output vcf, both tumoronly and germline produce a vcf that does not contain any variants, is that supposed to be the case? The vcf ends like this:

##TIDDITcmd="/usr/local/bin/tiddit --sv --skip_assembly --bam test.paired_end.recalibrated.sorted.cram --ref genome.fasta -o sample1" #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT normal

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FriederikeHanssen commented Jun 22, 2022 •
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Looks good. Subway map update is missing :)
Before we merge I will check on actual data that we are fine here. I suppose it is just that the text vcf doesn't contain SVs.

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WackerO commented Jun 22, 2022

Oh boy, I'll update the subway map and hope that Susi does not find any 0.1 nm wide bumps to complain about :*D
Sounds good!

@WackerO WackerO mentioned this pull request Jun 22, 2022
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FriederikeHanssen commented Jun 22, 2022

Almost there, one more thing missing, the tiddit output must be collected in the workflows/sarek similar to how Maxime has done this, in order to annotate the variants later:

        // Gather vcf files for annotation and QC
        vcf_to_annotate = Channel.empty()
        vcf_to_annotate = vcf_to_annotate.mix(GERMLINE_VARIANT_CALLING.out.deepvariant_vcf)
        vcf_to_annotate = vcf_to_annotate.mix(GERMLINE_VARIANT_CALLING.out.freebayes_vcf)
        vcf_to_annotate = vcf_to_annotate.mix(GERMLINE_VARIANT_CALLING.out.haplotypecaller_vcf)
        vcf_to_annotate = vcf_to_annotate.mix(GERMLINE_VARIANT_CALLING.out.manta_vcf)
        vcf_to_annotate = vcf_to_annotate.mix(GERMLINE_VARIANT_CALLING.out.tiddit_vcf)
        vcf_to_annotate = vcf_to_annotate.mix(GERMLINE_VARIANT_CALLING.out.strelka_vcf)
        vcf_to_annotate = vcf_to_annotate.mix(TUMOR_ONLY_VARIANT_CALLING.out.freebayes_vcf)
        vcf_to_annotate = vcf_to_annotate.mix(TUMOR_ONLY_VARIANT_CALLING.out.mutect2_vcf)
        vcf_to_annotate = vcf_to_annotate.mix(TUMOR_ONLY_VARIANT_CALLING.out.manta_vcf)
        vcf_to_annotate = vcf_to_annotate.mix(TUMOR_ONLY_VARIANT_CALLING.out.strelka_vcf)
        vcf_to_annotate = vcf_to_annotate.mix(PAIR_VARIANT_CALLING.out.mutect2_vcf)
        vcf_to_annotate = vcf_to_annotate.mix(PAIR_VARIANT_CALLING.out.manta_vcf)
        vcf_to_annotate = vcf_to_annotate.mix(PAIR_VARIANT_CALLING.out.strelka_vcf)
        ```

maxulysse
maxulysse reviewed Jun 23, 2022
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Comment thread subworkflows/local/tumor_variant_calling.nf Outdated
@FriederikeHanssen FriederikeHanssen merged commit cd503d1 into nf-core:dev Jun 23, 2022
@WackerO WackerO deleted the tiddit branch July 27, 2022 09:01
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