v0.1.13

Added

• Handling for GFF3 reference_annotation file type.
• Warning for the --transcriptome_source denovo pipeline option.

Changed

• Enum choices are enumerated in the --help output
• Enum choices are enumerated as part of the error message when a user has selected an invalid choice
• Bumped minimum required Nextflow version to 22.10.8

Fixed

• Replaced --threads option in fastqingress with hardcoded values to remove warning about undefined param.threads
• Fix for the --transcriptome_source denovo pipeline option.

v0.1.12

Added

• Handling for GFF3 reference_annotation file type.
• Handling gzip input reference and annotation parameters.
• Handling for NCBI gtfs that contain some empty transcript ID fields.

v0.1.11

Changed

• LICENSE to Oxford Nanopore Technologies PLC. Public License Version 1.0.

Added

• Configuration for running demo data in AWS

v0.1.10

Updated

• Condition sheet parameter description fixed to CSV
• Update fastqingress

v0.1.9

Updated

• Simplify JAFFAL docs

v0.1.8

Changed

• Updated description in manifest

v0.1.7

Updated

• -profile conda is no longer supported, users should use -profile standard (Docker) or -profile singularity instead
• nextflow run epi2me-labs/wf-transcriptomes --version will now print the workflow version number and exit
• Use parameter --transcriptome-source to define precalculated, reference-based or denovo

v0.1.6

Updated

• Removed sanitize option
• Reduce size of differential expression data.

Added

• Improved DE explanation in docs
• Option to turn off transcript assembly steps with param transcript_assembly

Fixed

• Fix JAFFAL terminating workflow when no fusions found.
• Error if condition sheet and sample sheet don't match.
• Failed to plot DE graphs when one of data sets is 0 length.

v0.1.5

Added

• Differential transcript and gene expression subworkflow

v0.1.4

Added

• JAFFAL fusion detectoion subworkflow

Changed

• Args parser for fastqingress
• Set out_dir option type to ensure output is written to correct directory on Windows
• Skip unnecessary conversion to fasta from fastq
• Fastqingress metadata map
• Changed workflow name to wf-transcriptomes