v3.1

[williamrowell]

Breaking Changes

• new static resource bundle v3.1.0 available from 10.5281/zenodo.17086906
  • updated recommended TRGT repeat catalog: adotto_strchive_20250827.hg38.bed.gz
  • new ref_map key: methbat_region_tsv with recommended value cpgIslandExt.sorted.hg38.tsv
• renamed outputs:
  • stat_num_reads -> stat_read_count
  • stat_mapped_percent -> stat_mapped_read_percent
  • stat_mean_depth -> stat_depth_mean

New Inputs

• optional sample input: Array[File]? fail_reads
• new ref_map key: methbat_region_tsv

New Outputs

• from new methbat task:
  • File? or Array[File?] methbat_profile
  • String or Array[String] stat_methbat_methylated_count
  • String or Array[String] stat_methbat_unmethylated_count
  • String or Array[String] stat_methbat_asm_count
• sawfish_call task:
  • File or Array[File] sv_copynum_summary
• bam_stats task:
  • String or Array[String] stat_gap_compressed_identity_mean
  • String or Array[String] stat_gap_compressed_identity_median

Change Log

• new Methbat task using v0.15.0 bump: Update Methbat to 0.15.0 #257
  • new added methbat_region_tsv input in ref_map
  • generates methbat_profile output with methylation status of defined CpG islands
• TRGT v4.0.0 bump: Update TRGT to v4.0.0 #245
  • added new optional fail_reads input, only used for TRGT genotyping; requires flagging regions in TRGT bed file for which to include fail_reads, as described in our TRGT documentation feat: Use fail_reads for TRGT #253
  • including fail_reads helps with sensitivity for some repeat expansions, notably FXN, RFC1, and FGF14
• Sawfish v2.1.1 bump: Update Sawfish to v2.1 #255
  • added new Copy-number summary output, useful for evaluating chromosome copy-number
• Paraphase v3.3.4 bump: Update Paraphase to v3.3.4 #247
• Mitorsaw v0.2.4 bump: Update Mitorsaw to v0.2.4 #256
• added read length n50 and gap-compressed identity mean/median to output stats Add read length n50 and mean gap-compressed identity to output stats. #254
• renamed some output stats for more consistent naming (e.g., <metric_name>_<count/mean/median>) Add read length n50 and mean gap-compressed identity to output stats. #254
• modified plotting/aggregation python scripts to use less memory fix: Reduce memory usage by pandas/matplotlib scripts #250

[juniper-lake]

changelog looks good