epi2me-labs/wf-transcriptomes: v2.0.0

This release refreshes wf-transcriptomes around a new reference-guided transcriptomics workflow built on bambu, with SQANTI3 transcript classification and QC, DESeq2 for differential gene expression, DEXSeq for differential transcript usage, and per-sample modified base summarisation with modkit when modification tags are present in aligned BAMs.

Changed

• Replaced the previous StringTie/GffCompare/Salmon-based transcript discovery and quantification workflow with a bambu-based workflow.
• The main transcriptome result is now a shared cohort transcriptome built from all samples together.
• Per-sample transcriptome FASTA outputs are now supplemented with per-sample GTF files, count tables, transcript metadata and QC summaries.
• Differential gene expression now uses DESeq2.
• Differential transcript usage continues to use DEXSeq, now driven from the shared bambu outputs.
• Transcript classification and QC is now performed for both cohort and per-sample transcriptomes with SQANTI3.
• Workflow prerequisites and experimental design inputs are validated earlier to catch common setup issues sooner.
• Output structure has been reorganised around:
  • cohort/
  • samples/<alias>/
  • de_analysis/<contrast>/
• Differential analysis outputs are now grouped per contrast under de_analysis/<contrast>/.
• The workflow now supports two bambu modes via --transcriptome_mode:
  • discover
  • fixed_annotation
• Per-sample modified base summarisation from aligned BAMs containing MM and ML tags using modkit, including:
  • bedMethyl pileup
  • per-sample modification summary tables
  • per-modification bigWig tracks
• Reports have been refreshed with new components including:
  • Sample-level hierarchical clustering, PCA and distance heatmap plots
  • Contrast-level interactive volcano plots

Removed

• Dependence on the older StringTie/GffCompare/Salmon transcriptomics pathway.
• --transcriptome_source parameter; use --transcriptome_mode instead.
• --ref_transcriptome parameter; use --transcriptome_mode fixed_annotation together with --ref_genome and --ref_annotation.
• --threads parameter; advanced users may use Nextflow process selectors to override the preset per-process CPU and memory limits.