v1.4.0

Added

• BED files for the VNTR regions in hg19/hg38 from Severus.
  • The appropriate file will be automatically selected for the appropriate genome, unless a user provides a custom bed with --tr_bed.
• IGV configuration supporting VCF files from --snv and --sv.
• Aligned BAM to the output, when re-alignment is required.

Changed

• Tweaked parameters for Severus to refine SV calling.
• More informative log when a BAM called with an invalid basecaller model is provided.
• Failures of processes involved in differentially modified loci and regions detection will not cause workflow to fail.
• Updated modkit to v0.3.3.
• Reconciled workflow _ingress.nf from wf-human-variation v2.4.0 and wf-template v5.2.6.

Fixed

• -resume failing for some snv processes.
• Excessive memory usage for sample_probs process when using --mod leading to exit code 137.
• Erroneous handling of inputs for the joint report.
• Missing re-aligned XAM files in the output directory.