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remove params from subworkflows #1359

Merged
merged 16 commits into from
Jan 10, 2024
Merged

remove params from subworkflows #1359

merged 16 commits into from
Jan 10, 2024

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maxulysse
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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/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 --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 19, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit eb52c68

+| ✅ 146 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • 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
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/sarek/sarek/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.11.1
  • Run at 2023-12-20 17:04:39

@maxulysse maxulysse marked this pull request as ready for review December 20, 2023 13:17
@edmundmiller edmundmiller mentioned this pull request Dec 22, 2023
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FriederikeHanssen
FriederikeHanssen reviewed Jan 10, 2024
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subworkflows/local/prepare_intervals/main.nf
Comment on lines +32 to +34
file("${outdir}/no_intervals.bed").text = "no_intervals\n"
file("${outdir}/no_intervals.bed.gz").text = "no_intervals\n"
file("${outdir}/no_intervals.bed.gz.tbi").text = "no_intervals\n"
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I am wondering actually if we could dump this into the work dir in the long run.

FriederikeHanssen
FriederikeHanssen reviewed Jan 10, 2024
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tests/test_intervals.yml
Comment on lines -141 to -142
- path: results/reference/intervals
should_exist: false
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so it exists?

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yeah something weird is happening there, and I went done a rabbit hole and gave up and I'll fix this in future PR

FriederikeHanssen
FriederikeHanssen reviewed Jan 10, 2024
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workflows/sarek.nf
Comment on lines -86 to -89
ascat_alleles = params.ascat_alleles ? Channel.fromPath(params.ascat_alleles).collect() : Channel.empty()
ascat_loci = params.ascat_loci ? Channel.fromPath(params.ascat_loci).collect() : Channel.empty()
ascat_loci_gc = params.ascat_loci_gc ? Channel.fromPath(params.ascat_loci_gc).collect() : Channel.value([])
ascat_loci_rt = params.ascat_loci_rt ? Channel.fromPath(params.ascat_loci_rt).collect() : Channel.value([])
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I see what you are doing. I would love if we can find a solution in the future where the file channel building happens in one place and not scattered.

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so do I

FriederikeHanssen
FriederikeHanssen approved these changes Jan 10, 2024
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Looks super good

@maxulysse
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Looks super good

Thanks

@maxulysse maxulysse merged commit 8b492b4 into nf-core:dev Jan 10, 2024
46 of 51 checks passed
@maxulysse maxulysse deleted the no_params branch January 10, 2024 15:10
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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@maxulysse @FriederikeHanssen