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.

v1.1.1

Changed

• Improved handling of different annotation file types (eg. .gtf/.gff/.gff3) in de_analysis mode.
• Improved handling of annotation files that do not contain version numbers in transcript_id (such as gtf's from Ensembl).

Fixed

• Differential expression failing with 10 or more samples.
• Regression causing the DE analysis numeric parameters to not be evaluated correctly.

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.

v1.0.0

Added

• Published minimap2 and pychopper results to output directory.
• Two extra pychopper parameters --cdna_kit and --pychopper_backend. --pychopper_options is still available to define any other options.
• Memory requirements for each process.

Changed

• Documentation.

Fixed

• When Jaffa is run only output one report.

v0.4.2

Changed

• Sample sheet must include a control type to indicate which samples are the reference for the differential expression pipeline.

Removed

• Default local executor CPU and RAM limits.

v0.4.1

Changed

• Updated docker container with Pychopper to support LSK114.

v0.4.0

Fixed

• Remove dead links from README

Removed

• Denovo --transcriptome_source option.