Version 2.1.3

• Upgrade image with new version of Scripts
• Fix bug when only one modality is given to quantify-by

Version 2.1.2

Changelog

• Fixed bug in max resources settings

Version 2.1.1

Changelog

• Added --feelnc-filter-args, --feelnc-codpot-args, --feelnc-classifier-args to pass arguments to every FEELnc script.
• Fixed expression clustering to work with any number of samples.
• Updated resource requirements for processes.

Version 2.1.0

Changelog

• Added Tmerge by default instead of StringTie to coalesce assembled transcripts into a novel annotation.
• Added --coalesce-transcripts-with to select the tool used to coalesce transcripts.
• Added --min-monoexonic-occurrence and --min-monoexonic-tpm to filter rare monoexonic transcripts separately after assembly.
• Added hierarchical clustering on genes TPM to compare quantification groups.
• Updated dependencies:
  • MultiQC 1.9 -> 1.12
  • STAR 2.7.9a -> 2.7.10a
  • Subread 1.6.0 -> 2.0.1

Version 2.0.0

Changelog

• Rewrote the pipeline in Nextflow DSL2.
• Added --assemble-by and --quantify-by to merge aligned reads separately for transcripts assembly and quantification.
• Added --min-transcript-occurrence and --min-transcript-tpm to filter rare transcripts after transcripts assembly.
• Added --skip-assembly to run the pipeline without generating a novel annotation.
• Added control plots to the MultiQC report.

Version 1.0.2

Changelog

• Updated a dependency in the container to correct long non-coding transcript counts in the multiQC report.

Version 1.0.1

Changelog

• Corrected gene and transcript counts in the annotation comparison section of the multiQC report.

Version 1.0.0

First official production-ready release.

Version 0.3.1

Fix unnecessary globbing of single files

Version 0.3.0

Add parameter check for --lncMode