Release/0.7.1 - #60
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* add ref data for pcgr 2.2.1 * add vep path pcgr * edit refdata path for vep pcgr * update pcgr report name name * change path VEP ref data * update container version * remove VEP version * change bolt version to test
* add process and config for vcf2maf * fix path vep data * remove duplicate * fix and linting * remove params from VCF2MAF process * fix and simplify process * add meta.key to channel * add genome build as input * add dockerfile * Make sigrap (HRDetect, MutationalPatterns) individual process (#16) * remove trace of genome build and hardcode in VCF2MAF * use biocontainers container for vcf2maf * remove string interpolation * change to stub no version template * revert deleted line
* change sigrap container * change cancer report container * latest bolt version * update meta id sigrap * bump sigrap * remove print * restaure metadata sigrap * change multiqc container * add param for pcgr chunck size * add mutpat predefined dbs argument * update container * add back formating comment
* fix channel prepare reference * refactor tarball extraction to use proper channel patterns. Follow oncoanalyser pattern for tarball extraction with .collect() and .map() * adapte extraction tarball to match pcgr expected vep structure * fix dir name extract tarball for VEP * change to adapt strip compoment for pcgr data
ghcr.io/umccr/bolt:0.3.0
* allow explicit DRAGEN VCF paths in samplesheet Add optional dragen_somatic_vcf and dragen_germline_vcf samplesheet filetypes. When present, they override the path constructed from tumor_id/normal_id. Enables cohorts where DRAGEN and oncoanalyser outputs use different sample ID prefixes (e.g. APGI). Add nf-tests covering default path construction and explicit override. * chore: add TODO to document new dragen vcf filetypes in usage.md * fix dragen relative path from sample sheet
…#54) * fix process PAVE_SOMATIC checks for MNVTAG in the VCF header before filtering * fix MNVTAG filter: use variable input path and add nf-tests - Replace cp with direct variable pass-through when MNVTAG absent (no disk copy, works on ICAv2 GDS and AWS Batch) - Fix typo: mnv_filtred -> mnv_filtered - Remove unnecessary intermediate file cleanup - Add stub nf-tests with fixtures for with/without MNVTAG header cases - Add .nf-test/ and .nf-test.log to .gitignore
Resolve conflicts keeping 0.7.0 versions for all bolt containers and version fields. Merge CHANGELOG to include 0.6.4 release from main.
- Fix label syntax: split 'process_medium_memory', 'process_long' into separate label directives (sigrap/mutpat, bolt/cancer_report, bolt/annotate) - Remove unused args declaration in sigrap/mutpat and sigrap/hrdetect - Fix ch_misc_data_channel to value channel with .first() so reference data is broadcast across all samples, not just the first - Remove path '.command.*' from extract_tarball outputs (captures internal Nextflow debug files, not workflow results) - Hardcode vcf2maf version to 1.6.22 (--help exits non-zero, unreliable) - Fix trailing whitespace in prepare_input.nf CHORD path lines
- Document optional dragen_somatic_vcf/dragen_germline_vcf samplesheet fields with example - Document pcgr_variant_chunk_size parameter for hypermutated samples - Update citation version from 0.6.0 to 0.7.0
…vent PURPLE receiving mnv_filtered intermediate
Ships the graceful PCGR skip on samples whose per-chunk variant count exceeds MAX_SOMATIC_VARIANTS, plus disable_estimates on chunked runs where MSI/TMB on partial VCFs is meaningless. Variant tag suffixes (-pcgr, -circos, -multiqc, -gpgr, -snpeff) preserved.
Moves hrdetect and mutpat modules off the personal docker.io/qclayssen dev build to the official umccr ghcr release image.
…ash #39) Address Stephen's review: remove the dead else-branch that handled plain directory miscdata_paths inputs. Tarballs are now the only supported mode for pcgr_dir/vep_dir — a clear error is raised if no tarball entries are found in miscdata_paths. Adds nf-test for the tarball extraction path (prepare_reference subworkflow). BREAKING CHANGE: miscdata_paths entries requiring extraction (pcgr_dir, vep_dir) must be provided as .tar.gz/.tgz archives. Plain directory inputs are no longer supported.
4 tasks
Reflects the current bolt 0.3.x tiered filtering approach (replaces outdated bolt v0.2.18 select_variants description). Documents the two silent failure modes in PCGR (Python-side variant drop + R-side HTML skip) that justify the 450k threshold. References bolt/docs/adr/001-max-somatic-variants-450k.md for the detailed boundary analysis.
…es (#59) When bolt PASS VCF exceeds 450k variants, select_pcgr_variants raises RuntimeError and PCGR is skipped. Mark pcgr_pass_vcf, pcgr_dir, and pcgr_report as optional so the process exits 0 and non-PCGR outputs (stats, AFs, counts) are still published for gpgr. Filter the VCF2MAF input channel to skip samples where pcgr_pass_vcf was not emitted. Closes #52
…t samples BOLT_SMLV_SOMATIC_REPORT unconditionally moved output/pcgr/*.html, which does not exist when PCGR/VCF2MAF are skipped for samples exceeding the sash #59 variant-count cap (ADR-001) -- causing the whole process to hard-fail on exactly the samples that skip is meant to handle. Adds nf-test coverage: optional PCGR emits let the process exit 0 when skipped, and the vcf2maf_input_filter channel chain drops the skipped sample's null entry before it reaches VCF2MAF.
bolt's actual safety threshold is 450,000 (MAX_SOMATIC_VARIANTS), not 500,000 (PCGR's own hard limit, which bolt stays under). Also documents that the Hypermutated flag is computed from the raw DRAGEN count and can trip on non-PASS noise alone, without any TMB-affecting filtering having occurred - verified against a real sample's FILTER tag counts.
bcftools view -h | grep -q could receive SIGPIPE mid-write on large real VCF headers (thousands of ##contig lines); under pipefail this flipped the if to the else branch even when MNVTAG was present, feeding unfiltered variants into PAVE 1.8. Write the header to a file first so there's no pipe for pipefail to trip on. Adds a standalone regression test that reproduces the race against a synthetic large header and confirms the fix. Fixes #66
1 task
Exercises the actual script: block against ghcr.io/umccr/bolt:0.3.2-pcgr, covering the mv output/pcgr/*.html guard fix (sash #59 / ADR-001) that stub-mode tests can't reach since -stub bypasses script: entirely.
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Release 0.7.1
Patch release: bolt 0.3.1 → 0.3.2.
Fixed
Dependencies
Prerequisite PRs
Relationship to 0.7.0
sash 0.7.0 (PR #39, bolt 0.3.1 + sigrap 0.3.0) is validated — Jijuan ran the PDAC cohort through sash 0.7.0 and validated the results. PR #39 is ready to merge; 0.7.1 can land after 0.7.0.