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feat added specific values for some samplesheet params #459

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Merged
merged 5 commits into from
Dec 22, 2023
Merged

feat added specific values for some samplesheet params #459

merged 5 commits into from
Dec 22, 2023

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@Lucpen
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@Lucpen Lucpen commented Dec 20, 2023

PR checklist

  • Restricted possible values in Samplesheet column sex and phenotype to [0,1,2]
  • 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 Dec 20, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 5a2c55c

+| ✅ 155 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowRaredisease.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • 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 2.11.1
  • Run at 2023-12-22 06:22:24

@Lucpen Lucpen added the ready for review PR is ready for review label Dec 21, 2023
@Lucpen Lucpen requested a review from jemten December 21, 2023 10:34
jemten
jemten reviewed Dec 21, 2023
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Nice work Lucia. I just remembered that we are using sex in some operations in the config files:

raredisease/conf/modules/generate_cytosure_files.config

Line 38 in e3160e5

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

raredisease/conf/modules/call_repeat_expansions.config

Line 27 in e3160e5

ext.args = { ("${meta.sex}" == '1') ? '--sex male' : '--sex female' }

I think these operations relies on the value being a string. Could you check and in that case remove the quotation marks?

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Lucpen commented Dec 22, 2023

Good catch!

@Lucpen Lucpen requested a review from jemten December 22, 2023 08:54
jemten
jemten approved these changes Dec 22, 2023
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👍

@Lucpen Lucpen merged commit 42f9d64 into nf-core:dev Dec 22, 2023
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@Lucpen @jemten