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@epi2melabs-bot epi2melabs-bot released this 04 May 08:14
· 86 commits to master since this release
v2.2.0
5651930

Added

  • Output {{sample}}.stats.json file describing some key metrics for the analysis.
  • Summary of gene coverage if a 4-column BED is provided.
  • Automated sex determination using relative coverage of chrX and chrY.
  • Retry strategy added to snp:aggregate_pileup_variants to prevent out of memory error.

Changed

  • --GVCF --phased will produce a phased GVCF.
  • Changed default phasing algorithm to whatshap, with the possibility to change the phasing to longphase with --use_longphase true.
    • The intermediate phasing is still performed using longphase.
  • Setting --snp --sv --phased will emit individually phased SNPs and SVs.
  • Phased bedMethyl files now follow the pattern {{ alias }}.wf_mods.{{ haplotype }}.bedmethyl.gz.
  • --sex parameter uses XX and XY rather than "female" and "male".
  • Update modkit to v0.2.6.
  • Improved modkit runtime by increasing default threads and increasing the default interval size.
  • Improved modkit runtime by increasing the default interval size and running modkit on individual contigs.
  • modkit is now run only on chromosomes 1-22, X, Y and MT, unless --include_all_ctgs is provided.
  • Increased minimum CPU requirement for the workflow to 16.
  • Filtering of SVs using a BED file now includes sites only partially overlapping the specified regions.
  • basecaller_cfg will be inferred from the basecall_model DS key of input read groups, if available
    • Providing --basecaller_cfg will not be required if basecall_model is present in the DS tag of the read groups of the input BAM
    • --basecaller_cfg will be ignored if a basecall_model is found in the input BAM
  • Reconciled workflow with wf-template v5.1.2
  • Update to Clair3 v1.0.8.
  • Update to longphase v1.7.1.

Fixed

  • Update schema to allow selection of multiple BAM files per sample in EPI2ME.
  • Spectre CNV report not handling cases when no CNVs detected.
  • Lines denoting normal maximum and pathogenic minimum thresholds now correctly displayed on STR repeat content plots.
  • Workflow will not emit sample.cram if sample.haplotagged.cram has been created by the workflow to save storage.
  • Emitting nonsense input.1 file

Removed

  • Single-step joint phasing of SV and SNP.
  • --output_separate_phased as the workflow emits only individually phased VCFs.
  • A copy of the reference and the generated reference cache is no longer output by the workflow.
    • The workflow encourages use of readily available standard reference sequences, so re-emitting the input reference as a workflow output is unnecessarily consuming disk space.
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