v1.1.0

Changed

• Improve documentation around filtering of transcripts done before DTU analysis.
• Renamed files:
  • de_analysis/all_counts_filtered.tsv to de_analysis/filtered_transcript_counts_with_genes.tsv
  • de_analysis/de_tpm_transcript_counts.tsv to de_analysis/unfiltered_tpm_transcript_counts.tsv
• Minimum memory requirements to 32 GB.

Added

• Published isoforms table to output directory.
• Output additional de_analysis/cpm_gene_counts.tsv with counts per million gene counts.
• Output additional de_analysis/unfiltered_transcript_counts_with_genes.tsv with unfiltered transcript counts with associated gene IDs.
• Add gene name column to the de_analysis counts TSV files.

Fixed

• Mapping stage using a single thread only.

Changed

• More memory assigned to the fusion detection process.
• When no --ref_annotation is provided the workflow will still run but the output transcripts will not be annotated. However --de_analysis mode still requires a --ref_annotation.