v0.3.0

Added

• Experimental guppy subworkflow
  • We do not provide a Docker container for Guppy at this time, users will need to override process.withLabel:wf_guppy.container

Changed

• --ubam option removed, users can now pass unaligned or aligned BAM (or CRAM) to --bam
  • If the input BAM is aligned and the provided --ref does not match the SQ lines (exact match to name and size) the file will be realigned to --ref
  • If the input CRAM is aligned and the provided --ref does not match the SQ lines (exact match to name and size) the file will be realigned to --ref, but will also require the old reference to be provided with --old_ref to avoid reference lookups
  • If the input is not aligned, the file will be aligned to --ref

Fixed

• Chunks without variants will no longer terminate the workflow at the create_candidates step

v0.2.2

Fixed

• "No such property" when using the minimap2_ubam alignment step
• Slow performance on minimap2_ubam step when providing CRAM as --ubam
• Slow performance on snp:readStats process

Removed

• "Missing reference index" warning was unnecessary

v0.2.1

Fixed

• "No such property" when using the minimap2_ubam alignment step
• Slow performance on minimap2_ubam step when providing uCRAM

Removed

• "Missing reference index" warning was unnecessary

v0.2.0

Added

• An experimental methylation subworkflow has been integrated, using modbam2bed to aggregate modified base counts (input BAM should have MM and ML tags), enable this with --methyl

Changed

• Workflow experimentally supports CRAM as input, uBAM input uses CRAM for intermediate files
• Reference FAI is now created if it does not exist, rather than raising an error
• --sniffles_args may be used to provide custom arguments to the sniffles2 process
• Output files are uniformly prefixed with --sample_name

Fixed

• Existence of Clair3 model directory is checked before starting workflow
• --GVCF and --include_all_ctgs are correctly typed as booleans
  • --GVCF now outputs GVCF files to the output directory as intended
  • --include_all_ctgs no longer needs to be set as --include_all_ctgs y

v0.1.1

Added

• --ubam_bam2fq_threads and --ubam_sort_threads allow finer control over the resourcing of the alignment step
  • The number of CPU required for minimap2_ubam is sum(ubam_bam2fq_threads, ubam_map_threads, ubam_sort_threads)

Changed

• --ubam_threads is now --ubam_map_threads and only sets the threads for the mapping specifically
• --ref is now required by the schema, preventing obscure errors when it is not provided
• Print helpful warning if neither --snp or --sv have been specified
• Fastqingress metadata map
• Disable dag creation by default to suppress graphviz warning

Fixed

• Tandem repeat BED is now correctly set by --tr_bed
• Update fastcat dependency to 0.4.11 to catch cases where input FASTQ cannot be read
• Sanitize fastq intermittent null object error

Note

• Switched to "new flavour" CI, meaning that containers are released from workflows independently

v0.1.0

Added

• Ported wf-human-snp (v0.3.2) to modules/wf-human-snp
• Ported wf-human-sv (v0.1.0) to modules/wf-human-sv