v1.7.2

This patch release of wf-transcriptomes updates internal workflow naming, and does not affect any workflow outputs.

Changed

• Removed workflow suffix from workflow title. This has no effect on the workflow.

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.

v1.7.0

Changed

• split_bam and build_minimap_index_transcriptome process memory allocation increased.
• Updated recommended memory requirement.
• Updated project description.
• A common user issue is providing a ref_annotation and ref_genome parameter that have mismatched reference IDs, which causes the DE_analysis to fail. The workflow will now do an upfront check and give an error message if no overlap is found or a warning if some IDs are present in one file but not in the other.
• Reconciled workflow with wf-template v5.5.0.
• Sort the columns and rows of the gene and transcript count files.
• DE_analysis alignment summary stats table no longer includes MAPQ or quality scores. MAPQ is not relevant for transcript alignment and quality scores are already available in the read summary section of the report.

Fixed

• all_gene_counts.tsv contained the DE counts results.
• Reduced memory usage of the report workflow process.
• Output BAM alignments in all cases unless the workflow is run with transcriptome_source set to precomputed.
• Corrected the demo command in the README.md.
• The merged transcriptome generated for differential expression analysis now only contains the exons and not the full genomic sequence.
• Output the gene name annotated differential expression analysis count files only.
• Only use full length reads in the differential expression analysis.

v1.6.1

Fixed

• merge_gff_compare failing with empty GFF files.

v1.6.0

Fixed

• v1.5.0 bug; access to undefined channel output bug when using precomputed transcriptome.
• Bug where incorrect gene_id assigned in the DE tables.

v1.5.0

Updated

• Workflow report updated to use ezcharts.

Fixed

• Exons per isoforms histogram reporting incorrect numbers.
• Output the results_dexseq.tsv file when --de_analysis enabled.

Removed

• per-class gffcompare tracking files as there exists a combine tracking file.

v1.4.0

Added

• --igv parameter (default: false) for outputting IGV config allowing visualisation of read alignments in the EPI2ME App.
• If required for IGV, reference indexes are output in to a igv_reference directory

Changed

• BAMS are output in to a BAMS directory.
• Reconcile with template 5.2.6.

v1.3.0

Removed

• Fusion detection subworkflow, as the functionality is not robust enough for general use at this time.

Changed

• Updated pychopper to 2.7.10

Added

• new cdna_kit options: PCS114 and PCB111/114

v1.2.1

Changed

• Increase some memory and CPU allocations.

v1.2.0

Added

• Workflow now accepts BAM or FASTQ files as input (using the --bam or --fastq parameters, respectively).

Changed

• MA plot in the results_dge.pdf has been updated to match the MA plot in the report.