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.

v0.3.1

Added

• Handling for input reference transcriptome headers that contain |

v0.3.0

Changed

• Improve differential expression outputs.
• Include transcript and gene count tables in DE_final folder.
• If differential expression subworkflow is used a non redundant transcriptome will be output which includes novel transcripts.
• Added wording to the report about how to identify novel transcripts in the DE tables.
• Nextflow minimum required version to 23.04.2
• --minimap_index_opts parameter has been changed to minimap2_index_opts for consistency.

Added

• An additional gene name column to the differential gene expression results. This is especially handy for transcriptomes where the gene ID is not the same as gene name (e.g. Ensembl).
• Wording to the report about how to identify novel transcripts in the DE tables.

v0.2.1

Changed

• Any sample aliases that contain spaces will be replaced with underscores.
• Updated documentation to explain we only support Ensembl, NCBI and ENCODE annotation file types.

Fixed

• Documentation parameter examples corrected.
• Handling for annotation files that use gene as gene_id attribute.
• Handling for Ensembl annotation files.

v0.2.0

Changed

• GitHub issue templates
• Condition sheet is no longer required. The sample sheet is now used to indicate condition instead.
  • For differential expression, the sample sheet must have a condition column to indicate which condition group each sample in the sample sheet belongs to.
  • Values for the condition may be any two distinct strings, for example: treated/untreated; sample/control etc.

Fixed

• Remove default of null for --ref_transcriptome.
• Read mapping summary table in the report has correct sample_ids.