v1.2.0

Added

• Support for input folders of BAM files for --bam_tumor and --bam_normal (instead of only allowing single BAM files).

Changed

• ClinVar version in SnpEff container updated to version 20240307
• Update to Clair3 v1.0.7.
• Update to modkit v0.2.6.
• Improved modkit runtime by increasing the default interval size.
• Increased minimum CPU requirement for the workflow to 16.
• bedMethyl output files now follow the pattern {{ alias }}.wf-somatic-mods.{{ type }}.bedmethyl.gz.
• Structural variant (SV) calling is now performed with Severus (v0.1.2).
• ARM-compatible base workflow and modified base calling.
• minimap2 alignments will be in BAM format when --sv is set.

Fixed

• Force minimap2 to clean up memory more aggressively. Empirically this reduces peak-memory use over the course of execution.
• Workflow occasionally repeating QC analyses when resuming, even if successful.
• Alignment report script using too much memory.
• HAC models not recognised as valid.
• Spurious bamstats crashes with implausible alignment information.

Removed

• CRAM as supported input format.
• Reference genome and its indexes from the output directory.
• Insert classification and support for mismatching panel of control.
• Options --qv, --classify_insert, --min_ref_support, --genotype_sv and --control_panel, as these are no longer used by the workflow.