The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
Initial release of QUANTS, created with the nf-core template.
- Rename from nf-core-sge to QUANTS
- Fix SeqPrep->QC file assignment bug
- Add initial documentation
- Restructure flow of data (technical debt)
- Add subflow for read transform (rev comp, rev, comp)
- Add support for CRAM input
- Remove separate library-independent quantification
- Replace library-dependent quantification with counting unqiue reads + merge with library (pyCROQUET)
- Allow sample names to start with numeric in post-processing R script
- Remove meta id tag from pyCROQUET module
- Replace pyCROQUET with pyQUEST version 1.0
- Add script for converting VaLiAnT meta file (or other CSV/TSV) into pyQUEST-formatted library (not integrated into workflow)
- Split read trimming into two stages
- Adapter trimming - removes user-defined adapter sequences and takes forward both trimmed and untrimmed reads
- Primer trimming - removes user-defined primer sequences and takes forward only trimmed reads
- Add a read modification process which can append user-defined sequences to trimmed reads
- Add library transformer to allow users to provide libraries in a different format (e.g. the meta CSV from VaLiAnT) and convert it for use with pyQUEST
- Primer trimming - bugfix to ensure cutadapt splits reads into trimmed and untrimmed files
- Collation of cutadapt JSON results into single JSON file
- Collation of SeqKit statistics results into a single TSV file
- Update version of pyQUEST to version 1.1.0
- Improved handling of 0-length reads
- Ability to extract top 50 library-independent counts as FASTA
- Hotfix to force COLLATE_CUTADAPT_JSONS to run on 1 cpu