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.

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