epi2me-labs/wf-transcriptomes: v1.7.1

Changed

• Updated to wf-template v5.6.2, changing:
  • Reduce verbosity of debug logging from fastcat which can occasionally occlude errors found in FASTQ files during ingress.
  • Log banner art to say "EPI2ME" instead of "EPI2ME Labs" to match current branding. This has no effect on the workflow outputs.
  • pre-commit configuration to resolve an internal dependency problem with flake8. This has no effect on the workflow.
• Stringtie updated to v2.2.3, which fixes stalling at transcriptome assembly step.
• Gffcompare updated to v0.12.6, which fixes issue where ref_gene_id was assigned an nan value.

Fixed

• Updated to wf-template v5.6.2, fixing:
  • Sequence summary read length N50 incorrectly displayed minimum read length, it now correctly shows the N50.
  • Sequence summary component alignment and coverage plots failed to plot under some conditions.
• Error in deAnalysis process - mode(counts) %in% "numeric" is not TRUE - caused by hyphens in sample sheet aliases.
• Error in deAnalysis process - values in 'transcripts$tx_strand' must be "+" or "-".
  • The workflow will now filter out any unstranded annotations from downstream analysis and log a warning.
• Missing results_dexseq.tsv file when --de_analysis enabled.