nf-cmgg/exomecnv: Changelog

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

v1.2.0 - Dominant De Ketelaere [2024-11-27]

`Updates`

Bumped the template to nf-core v3.0.2

`Improvements`

Refactored the whole pipeline and made some small improvements
Removed a bottleneck in the exomedepth flow
Samplesheet header: rename pool to batch (issue/23)

v1.1.0 - Amazing Alderweireld [2024-11-19]

`Improvements`

SAMTOOLS_CONVERT: add optional output path for BAM files
copy samplesheet.csv to output dir
add pipeline testing with nf-test
bedgovcf module config: add format field
exomedepth/merge_count module: sort columns in summary file by sample names

`Updates`

Bumped modules utils_nextflow_pipeline, bedgovcf, ensemblvep/vep, multiqc, tabix/tabixand samtools/convert to the newest versions
Upgraded nf-core to v3.0.2 template
Upgraded nextflow version to 24.10.0

v1.0.2 - Youthful Yamal [2024-07-10]

`Fixes`

CNV_CALL_X: fix input channel to "roi_chrx"
allow sample numbers as sample names

v1.0.1 - Lightning Lukaku [2024-06-19]

`Improvements`

Index the VEP annotated VCF with TABIX
Do not copy output of SAMTOOLS_CONVERT module (BAM files) to the publishDir
update versions of multiqc and samtools_convert modules
optimize module resources

`Fixes`

Sort file of merged CNV calls to fix an issue with TABIX (needs sorted VCF files)

v1.0.0 - Dashing Doku - [2024-06-12]

Initial release of nf-cmgg/exomecnv, created with the nf-core template v2.13.

`Added`

First release of the pipeline - CNV calling using ExomeDepth