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Prevent pipeline fails from erroneous param validation of fasta and … #392

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merged 1 commit into from
Nov 20, 2024
Merged

Prevent pipeline fails from erroneous param validation of fasta and … #392

merged 1 commit into from
Nov 20, 2024

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bjlang
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@bjlang bjlang commented Nov 20, 2024 •
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…gtf parameters if iGenomes are used

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/atacseq 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 Nov 20, 2024 •
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nf-core pipelines lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 75378f5

+| ✅ 233 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   7 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 nextflow.config: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs
  • 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 base.config: Check the defaults for all processes
  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • nextflow_config - Config default ignored: params.bamtools_filter_pe_config
  • nextflow_config - Config default ignored: params.bamtools_filter_se_config

✅ Tests passed:

Run details

  • nf-core/tools version 3.0.2
  • Run at 2024-11-20 13:24:02

mirpedrol
mirpedrol approved these changes Nov 20, 2024
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subworkflows/local/utils_nfcore_atacseq_pipeline/main.nf
//
// Validate channels from input samplesheet
//
def validateInputSamplesheet(input) {
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Is this function not used?

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No. RNAseq, which we use as reference isn't using it either.

assets/samplesheet_with_control.csv
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Just a heads-up that this file change, and it doesn't seem to be related to the PR, in case it was changed by mistake.

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You're right. It's unrelated, but still correct to create coherence with assets/samplesheet.csv

@bjlang bjlang merged commit 2717572 into nf-core:dev Nov 20, 2024
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@bjlang @mirpedrol