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nf-test prepare_genome #1247

Merged
merged 5 commits into from
Mar 8, 2024
Merged

nf-test prepare_genome #1247

merged 5 commits into from
Mar 8, 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/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).

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github-actions bot commented Mar 8, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8551a0d

+| ✅ 169 tests passed       |+
#| ❔   8 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 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 methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.13.1
  • Run at 2024-03-08 16:05:21

@maxulysse maxulysse mentioned this pull request Mar 8, 2024
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adamrtalbot
adamrtalbot approved these changes Mar 8, 2024
View reviewed changes
subworkflows/local/prepare_genome/tests/main.nf.test
Comment on lines +44 to +68
input[0] = file(params.pipelines_testdata_base_path + 'reference/genome.fasta', checkIfExists: true)
input[1] = file(params.pipelines_testdata_base_path + 'reference/genes_with_empty_tid.gtf', checkIfExists: true)
input[2] = file(params.pipelines_testdata_base_path + 'reference/genes.gff', checkIfExists: true)
input[3] = file(params.pipelines_testdata_base_path + 'reference/gfp.fa', checkIfExists: true)
input[4] = file(params.pipelines_testdata_base_path + 'reference/transcriptome.fasta', checkIfExists: true)
input[5] = null
input[6] = null
input[7] = file(params.pipelines_testdata_base_path + 'reference/bbsplit_fasta_list.txt', checkIfExists: true)
input[8] = null
input[9] = null
input[10] = file(params.pipelines_testdata_base_path + 'reference/rsem.tar.gz', checkIfExists: true)
input[11] = file(params.pipelines_testdata_base_path + 'reference/salmon.tar.gz', checkIfExists: true)
input[12] = null
input[13] = file(params.pipelines_testdata_base_path + 'reference/hisat2.tar.gz', checkIfExists: true)
input[14] = null
input[15] = null
input[16] = gencode
input[17] = featurecounts_group_type
input[18] = aligner
input[19] = pseudo_aligner
input[20] = skip_gtf_filter
input[21] = skip_bbsplit
input[22] = skip_sortmerna
input[23] = skip_alignment
input[24] = skip_pseudo_alignment
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What an absolute unit.

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yeah, that's a subworkflow with a lot of inputs

@maxulysse maxulysse merged commit cd6d5ac into nf-core:dev Mar 8, 2024
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@adamrtalbot adamrtalbot linked an issue Mar 11, 2024 that may be closed by this pull request
Add nf-test to PREPARE_GENOME subworkflow #1178
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@adamrtalbot adamrtalbot mentioned this pull request Mar 11, 2024
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@adamrtalbot adamrtalbot adamrtalbot approved these changes

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Add nf-test to PREPARE_GENOME subworkflow
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@maxulysse @adamrtalbot