fix: Enhance RSEM output exports and remove unnecessary star_rsem check #1667
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Dev -> master for nf-core/rnaseq 3.22.0
Dev -> master for nf-core/rnaseq 3.22.1
Dev -> master for nf-core/rnaseq 3.22.2
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PR checklist
This comment contains a description of changes (with reason).
Remove unnecessary check for star_rsem unaligned BAM creation
STAR_RSEM automatically generates unaligned BAM files during the
quantification process, so this validation check is not needed.
Export additional RSEM quantification outputs for completeness
Added merged_genes_long and merged_isoforms_long to the emit block
in the QUANTIFY_RSEM workflow to preserve complete quantification
results for downstream analysis.
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 pipelines 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.mdis updated.Output Documentation in
docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).