2.0.0 - Rad Sepia

Initial release of (renamed) qbic-pipelines/vcftocounts.

Changed

• #25 - Rename pipeline to vcftocounts + Prepare Release 2.0.0
• #28 - Move test data to test-datasets, create filter nf-test

Added

• #22 - Remove ID column entries from VCFs
• #23 - Add filtering of VEP annotated VCF files using bcftools/view (no conda for NXF_VER <= 24.10.2)

Fixed

• #15 - template update to v3.1.1
• #16 - Fix bcftools/reheader bug
• #21 - template update to v3.2.0
• #24 - Change branching logic to enable caching again + rename vcf2mat to vcf2counts (thank you @awgymer for helping)

1.1.0 - Newton Puccoon

Added

• #7 - samplenames to columns
• #8 - concat for sample, label pairs

Fixed

• #5 - filename collision
• #10 - prepare release 1.1.0

1.0.0 - Curie Purpureal

This is the initial release of a pipeline that can take (g)VCF files and converts them a table format useful for statistical analysis.

1. Indexes (g.)vcf files (tabix)
2. Converts g.vcf files to vcf with genotypegvcf (GATK)
3. Merges all vcfs from the same sample with bcftools/merge (bcftools)
4. Converts the (merged) vcfs to a matrix using a custom R script written by @ellisdoro (R)
5. Collects all reports into a MultiQC report (MultiQC)