nf-core/rnaseq 3.5

nf-core/rnaseq v3.5 - Copper Chameleon

on GitHub

[3.5] - 2021-12-17

Enhancements & fixes

• Port pipeline to the updated Nextflow DSL2 syntax adopted on nf-core/modules
  • Removed --publish_dir_mode as it is no longer required for the new syntax
• Bump minimum Nextflow version from 21.04.0 -> 21.10.3
• Updated pipeline template to nf-core/tools 2.2
• [#664] - Conflict of library names for technical replicates
• [#720] - KeyError 'gene_id' in salmon_tx2gene.py
• [#724] - Deal with warnings generated when native NF processes are used
• [#725] - Untar needs --no-same-owner on DNAnexus
• [#727] - Fix transcriptome staging issues on DNAnexus for rsem/prepareference
• [#728] - Add RSeQC TIN.py as a quality metric for the pipeline