epi2me-labs/wf-human-variation: v2.8.0

This minor release of wf-human-variation updates modkit to improve the performance of modkit pileup processes for the base modifications subworkflow. On our HG002 dataset, the per-chromosome modkit_phase processes run 10x faster on average while still returning the same base modifications, with some minor differences to the score and count columns. The base modification subworkflow now also outputs bigWig files for more efficient downstream visualisation of 5mC calls. This version of the workflow may affect base modification results but variant calls in the other subworkflows are not affected. Additionally, this release of wf-human-variation updates the Clinvar database for more recent annotations and fixes a misleading error message about basecaller model detection when in fact the input data coverage is below threshold.

Users of the --mod base modification subworkflow are recommended to adopt this release to benefit from the performance improvement.

Changed

• Updated to modkit v0.6.1 to improve performance of modkit pileup processes.
  • When running with --mod --phased, modkit and wf-human-variation no longer outputs "ungrouped" modification counts. Instead, the {{ alias }}.wf_mods.bedmethyl.gz will contain counts tabulated from all records.
• Updated to wf-template v5.7.0 to maintain compliance with our latest wf-template standard, changing:
  • Pipeline overview now appears before pipeline parameters in README.
  • ezCharts plotting library has been updated to 0.15.1, there are no user facing changes to plots.
  • Fastcat FASTQ pre-processing program has been updated to 0.24.2, it is more robust to malformed FASTQ input.
  • CHANGELOG to be compliant with our formatting rules.
• The error when an input file has insufficient coverage for analysis and will not be processed by the workflow has been made more obvious in the log.
• ClinVar database updated to version 20260114.
• Cleaned up syntax for optional outputs defined in common.nf (@robsyme, #296), and other out-of-spec syntax preventing parsing by the Nextflow language server.
• Clarified in the Pipeline Overview that the workflow conducts alignment automatically where appropriate.

Fixed

• Reduced fatal memory errors ("Error: 137") encountered during the sample_probs process of the --mod subworkflow by increasing the memory allocation.
• cat_haplotagged_contigs re-run on resume unnecessarily (@raonyguimaraes, #295)
• Misleading "Input data error" implying the basecalling model could not be detected from an input when actually the input was discarded for having a depth below the bam_min_coverage threshold.

Added

• bigWig tracks for visualisation of 5mC counts are output when using the modification subworkflow.
• Workflow overview diagram in the documentation.

Removed

• When running with --mod --phased, {{ alias }}.wf_mods.ungrouped.bedmethyl.gz is no longer generated by modkit.