v2.4.1

Changed

• Reconciled workflow with wf-template v5.2.6

v2.4.0

Added

• IGV configuration for the EPI2ME App includes the output VCF files.

Changed

• Emit indexes for the input reference, when generated by the workflow.
• Links to the reference genomes in the README now point to bgzip-compressed fasta files.
• Updated modkit to v0.3.3.
• Reconciled workflow with wf-template v5.2.5

Fixed

• ERROR ~ No such variable: colors when the workflow cannot find the reference file.
• Incorrect bin size unit in QDNAseq wrapper script help text (@HudoGriz, #209).
• minimap2 version missing from alignment report.
• Resume crashing in some processes due to pre-existing directories.
• Expose additional arguments for specific tools.
• Excessive memory usage for sample_probs process when using --mod leading to exit code 137.
• aggregate_pileup_variants and aggregate_full_align_variants processes occasionally crashing with exit code 137.

v2.3.1

Fixed

• Handling of empty tr_bed parameter (@HudoGriz, #201)
• CNV VCF incorrectly annotated when --annotation false
• Remove comment lines from user supplied BED, to prevent the workflow crashing due to unrecognised columns
• 'implausible alignment information' encountered when workflow re-aligns an already aligned BAM.
• Automated basecaller detection not finding a basecaller model

Changed

• Alignment statistics are now reported for the regions in a BED file, if one is supplied by the user.

v2.3.0

Removed

• --basecaller_cfg is now redundant as the workflow automatically detects the basecall model from the input data since v2.2.0.

Added

• --override_basecaller_cfg parameter allows users to provide a basecall configuration name in cases where automatic basecall model detection fails.

Changed

• ClinVar version in SnpEff container updated to version 20240708.
• Updated demo data.

v2.2.6

Fixed

• ERROR_OUT_OF_CHROMOSOME_RANGE annotation in VCF on chrM variants due to different nomenclature used by SnpEff.

Changed

• Reconciled workflow with wf-template v5.2.0
• Removed FXN homopolymer region from list of STRs genotyped by --str sub-workflow

v2.2.5

Fixed

• Non-deterministic SNP output when --phased is on.
• Post-Clair3 whatshap phases only SNVs to match whatshap<2.0 behaviour.
• Updated ont-spectre to v0.2.2 to fix an apparent callCNV hang.
• Updated straglr to v1.4.5 to fix possible ZeroDivisionError during call_str.

Changed

• Updated modkit to v0.3.0.
• SV subworkflow publishes SNF file for onward multi-sample SV calling.

v2.2.4

Fixed

• sample_probs process failing when multiple modified base types are being analysed.
• --mod crashing when --phased false --str --cnv.

v2.2.3

Added

• Clair3 HAC and SUP V5.0.0 models

Changed

• Update Spectre to v0.2.1, which generates a predicted karyotype that is included in the HTML report.
• Improved reliability of the haplocheck process.

Fixed

• infer_sex causing SNP subworkflow to wait unnecessarily on completion of mosdepth
• Alignment QC report crashing due to missing unmapped histograms
• Unsupported [email protected] model
• Missing Clair3 mapping for v3.5.1 models
  • The missing model mapping is provided for completeness, users are strongly encouraged to re-basecall data on newer models to take advantage of significant improvements.

Changed

• Workflow will exit early with an informative message and alignment report if there are no aligned reads in the BAM

v2.2.2

Changed

• Workflow emitting OPTIONAL_FILE in some cases.
• File format of alignment files created by the workflow can be explicitly controlled with --output_xam_fmt [bam|cram].
  • The default is CRAM to match existing behaviour, for BAM use --output_xam_fmt bam.
• Enable RUST_BACKTRACE to automatically provide improved log messages for modkit issues.

Removed

• JBrowse configuration as it is no longer supported.
• Unused merge_threads parameter.

Fixed

• "No such file or directory" error for SV tandem repeat BED when user has assets in /data/

v2.2.1

Changed

• Reconciled workflow with wf-template v5.1.4

Fixed

• modkit sample-probs failing with downsampling and re-alignments.
• Workflow waiting for mosdepth and readStats processes when --bam_min_coverage 0.