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Add option to annotate vcf2cytosure file with different(customer) ids #521

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Merged
merged 5 commits into from
Mar 1, 2024
Merged

Add option to annotate vcf2cytosure file with different(customer) ids #521

merged 5 commits into from
Mar 1, 2024

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@ramprasadn
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@ramprasadn ramprasadn commented Feb 28, 2024

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 - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/raredisease 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 --outdir <OUTDIR>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>).
  • 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).

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github-actions bot commented Feb 28, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4f088f3

+| ✅ 176 tests passed       |+
#| ❔   7 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • readme - README contains the placeholder zenodo.XXXXXXX. This should be replaced with the zenodo doi (after the first release).
  • pipeline_todos - TODO string in main.nf: Optionally add in-text citation tools to this list.
  • pipeline_todos - TODO string in main.nf: Optionally add bibliographic entries to this list.
  • pipeline_todos - TODO string in main.nf: Only uncomment below if logic in toolCitationText/toolBibliographyText has been filled!
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-raredisease_logo_dark.png
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-01 12:49:45

@ramprasadn ramprasadn marked this pull request as ready for review February 28, 2024 22:41
@ramprasadn ramprasadn requested a review from jemten February 29, 2024 12:17
jemten
jemten reviewed Feb 29, 2024
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Question about sample meta, otherwise it looks good.

subworkflows/local/generate_cytosure_files.nf Outdated
ch_bam.combine(ch_vcf_tbi)
.map {
meta_sample, bam, meta_case, vcf, tbi ->
new_meta = ['id':meta_sample.sample]
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@jemten jemten Feb 29, 2024

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Won't this drop all the information that is in the bam meta aside from sample id? We need to preserve the sample meta as it contains information about the sample sex, which is used in the vcf2cytosure command, or att least transfer that key as well.

raredisease/conf/modules/generate_cytosure_files.config

Line 38 in 7e004ad

meta.sex.equals(1) ? '--sex male' : '--sex female',

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@ramprasadn ramprasadn Feb 29, 2024

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Aah, good catch! Will fix it.

jemten
jemten approved these changes Mar 1, 2024
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👍

@ramprasadn ramprasadn merged commit 4f02eb0 into nf-core:dev Mar 1, 2024
@ramprasadn ramprasadn deleted the vcf2cytosurerename branch March 18, 2024 10:33
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@jemten jemten jemten approved these changes

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@ramprasadn @jemten