CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing: Changelog

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

v1.2.0

Add fix for sample replicates with different split sizes
Add option to use samtools for duplicate marking
Updated modules
Updated to nf-core template v2.8
Fix issue where unaligned samples were not merged and fixed naming
Add minimal support for sample "tags" in sample sheet
Add panel coverage analysis
Limit panel coverage analyses to samples with WES/WGS tags
Make BAM_ARCHIVE accept channels with cram files
Drop ELPREP support
Add support for cram and index outputs in SAMTOOLS_SORMADUP
Add option to disable marking duplicates
Update to nf-core template v2.9
Start using nf-validation for input parsing
Drop support for generating aligner indices

v1.1.2

Support for bamprocessing with ELPREP
Improved sample grouping
Meta value clean up
bump modules
fix multiqc report to include all results
fix duplicate marking with bamsormadup
drop post alignment sorting, doesn't make sense as we do sort/markdup afterwards
Add option to use elprep for alignment postprocessing

v1.0.2dev

Add unaligned denominator to unaligned samples

v1.0.1

Updated modules

`Fixed`

Bug with fgbio/fastqtosam where having multiple files per read requires a read structure

v1.0dev - [06/09/2022]

Initial release of CenterForMedicalGeneticsGhent/nf-cmgg-preprocessing, created with the nf-core template.