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DRAFT: Allow any step but annotation to start from bam-files#654

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apeltzer merged 4 commits intonf-core:devfrom
asp8200:adjust_checks_step_plus_csv
Jul 18, 2022
Merged

DRAFT: Allow any step but annotation to start from bam-files#654
apeltzer merged 4 commits intonf-core:devfrom
asp8200:adjust_checks_step_plus_csv

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@asp8200 asp8200 commented Jul 18, 2022

This issue was reported by @nickhsmith :
Input csv:

patient,status,sample,lane,bam,bai
test,0,test,lane0,bam_path,bai_path

nf cmd:

nextflow run sarek --tools haplotypecaller --step variant_calling

Pipeline stopped with following msg:

Samplesheet contains ubam files but step is `variant_calling`. Please check your samplesheet or adjust the step parameter.
https://nf-co.re/sarek/usage#input-samplesheet-configurations

The pipeline shouldn't stop in such cases, in fact, @FriederikeHanssen pointed out that "almost any step can start from bam except for annotation which has to start from vcf".

With the change that I did now, the pipeline runs successfully with the above-mentioned input and command.

Further changes could perhaps be made for some of the other checks, but I don't like to change too many of these checks so close to our release date. Let me know what you think. Cheers

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).

@maxulysse
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maxulysse commented Jul 18, 2022

Looks good to me, can you update CHANGELOG.md too please?

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github-actions bot commented Jul 18, 2022 •
edited
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9be3c5c

+| ✅ 146 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 2022-07-18 19:20:10

@FriederikeHanssen FriederikeHanssen marked this pull request as ready for review July 18, 2022 18:32
@apeltzer apeltzer merged commit 3a0d841 into nf-core:dev Jul 18, 2022
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@apeltzer apeltzer apeltzer approved these changes

@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

@nickhsmith nickhsmith Awaiting requested review from nickhsmith

@maxulysse maxulysse Awaiting requested review from maxulysse maxulysse is a code owner

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@asp8200 @maxulysse @apeltzer @FriederikeHanssen