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Pass transcriptome fasta through to samtools stats #1213

Merged
merged 2 commits into from
Feb 16, 2024
Merged

Pass transcriptome fasta through to samtools stats #1213

merged 2 commits into from
Feb 16, 2024

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pinin4fjords
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We supply a reference FASTA to samtools stats to enable accurate mismatch, insertion, and deletion reporting by comparing aligned reads against the reference sequence, thereby enhancing the analysis of alignment quality and genomic variation. This facilitates a comprehensive assessment of the sequencing data, including coverage and variant analysis, by providing the precise genetic context for the reads.

So we must supply a reference compatible with the alignments. In the case of the transcriptome alignments, this should be the transcriptome.

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.
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github-actions bot commented Feb 16, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 34f57c0

+| ✅ 169 tests passed       |+
#| ❔  10 tests were ignored |#
!| ❗   5 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
  • files_exist - File not found: lib/WorkflowRnaseq.groovy
  • 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
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/Utils.groovy
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • nextflow_config - Config default ignored: params.ribo_database_manifest
  • 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 does not exist: lib/NfcoreTemplate.groovy
  • 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 2.12.1
  • Run at 2024-02-16 10:22:32

@pinin4fjords
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Thanks @maxulysse !

@pinin4fjords pinin4fjords merged commit 0cd5036 into dev Feb 16, 2024
27 checks passed
@pinin4fjords pinin4fjords deleted the transcriptome_stats branch February 16, 2024 12:42
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@maxulysse maxulysse maxulysse approved these changes

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@pinin4fjords @maxulysse