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Fix issues with unzipping of GTF/ GFF files without absolute paths #1312

Merged
merged 6 commits into from
Jun 18, 2024
Merged

Fix issues with unzipping of GTF/ GFF files without absolute paths #1312

merged 6 commits into from
Jun 18, 2024

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pinin4fjords
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Closes #1311

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/rnaseq 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>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,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).

@pinin4fjords pinin4fjords added this to the 3.15.0 milestone May 31, 2024
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github-actions bot commented May 31, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 191535b

+| ✅ 171 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • 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
  • 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!

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-06-18 14:21:31

@fbnrst
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fbnrst commented May 31, 2024

thanks @pinin4fjords

In #1311, I only provide a example for gtf, but I also mention that I saw the same issue for fasta files. Maybe we should have a look there as well. Possibly also --additional_fasta?

@fbnrst
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fbnrst commented May 31, 2024 •
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Yep, this lines might also need a fix:

rnaseq/subworkflows/local/prepare_genome/main.nf

Line 66 in b89fac3

ch_fasta = GUNZIP_FASTA ( [ [:], fasta ] ).gunzip.map { it[1] }

rnaseq/subworkflows/local/prepare_genome/main.nf

Line 106 in b89fac3

ch_add_fasta = GUNZIP_ADDITIONAL_FASTA ( [ [:], additional_fasta ] ).gunzip.map { it[1] }

@fbnrst
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fbnrst commented May 31, 2024

maybe even all related to those?

rnaseq/subworkflows/local/prepare_genome/main.nf

Lines 5 to 10 in b89fac3

include { GUNZIP as GUNZIP_FASTA } from '../../../modules/nf-core/gunzip'
include { GUNZIP as GUNZIP_GTF } from '../../../modules/nf-core/gunzip'
include { GUNZIP as GUNZIP_GFF } from '../../../modules/nf-core/gunzip'
include { GUNZIP as GUNZIP_GENE_BED } from '../../../modules/nf-core/gunzip'
include { GUNZIP as GUNZIP_TRANSCRIPT_FASTA } from '../../../modules/nf-core/gunzip'
include { GUNZIP as GUNZIP_ADDITIONAL_FASTA } from '../../../modules/nf-core/gunzip'

@pinin4fjords pinin4fjords enabled auto-merge June 18, 2024 14:27
@pinin4fjords pinin4fjords merged commit 292a80c into dev Jun 18, 2024
185 checks passed
@pinin4fjords pinin4fjords deleted the fix_gtf_unzip branch June 18, 2024 14:55
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@FriederikeHanssen FriederikeHanssen FriederikeHanssen approved these changes

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