v1.2.0 - Dominant De Ketelaere

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

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

Fixes

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

v1.0.1 - Lightning Lukaku

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

First release of the pipeline 💨 - CNV calling using ExomeDepth