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Release/0.6.1 (#23)
* Add docs OA v2.2.0 support, PAVE MNV filtering documentation and v0.6.1 changelog * oncoanalyser 2.2 support with PAVE mnv filtered (#21) * update linx version * bump pave version to 1.7.1 * update hmf_reference_data * Update ref data to match hmf_pipeline_resources.38_v2.2.0--3 * remove gridss_region_blocklist not used in sash * remove lilac reference data unused and fix isofox ones * remove orange reference data not used * update SAGE PON ref * remove unused sigs_signatures * remove deprecated disease_ontology refdata * - Bump eSVee from v1.0.3 to v1.1.2 - Bump LINX from v2.0.2 to v2.1 - Bump PAVE from v1.7.1 to v1.8 - Bump PURPLE from v4.1 to v4.2 * update PAVE process * update eSVee path * linting * add MNVTAG tag filter * fix sage path * fix esvee command * fix pave script * add bcftools pave container * Bump bolt version to V0.2.15 * change container adress for PAVE * Update modules/local/pave/somatic/main.nf Co-authored-by: Stephen Watts <[email protected]> * change pave docker file removing hardcoded platform and check symblink * remove deprecated line bcftool in pave * revert trailing comma prepare_ipunt * Change use directly biocontainer * Change pave dockerfile so it follow https://github.com/umccr/sash/blob/main/modules/local/purple/Dockerfile approach --------- Co-authored-by: Stephen Watts <[email protected]> * remove log level * revert pave container * fix bcftools version in sash * fix purple docker container * restore purple Dockerfile * fix typo * Bump version: 0.6.0 → 0.6.1 --------- Co-authored-by: Stephen Watts <[email protected]>
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‎.bumpversion.cfg‎

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[bumpversion]
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current_version = 0.6.0
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current_version = 0.6.1
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commit = True
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tag = False
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parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>[a-z0-9+]+)

‎CHANGELOG.md‎

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### `Deprecated`
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## [0.6.1] - 2025-09-16
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### Added
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- Support for oncoanalyser v2.2.0 data structure
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- PAVE MNV filtering to remove variants with MNVTAG annotations (see [discussion](https://github.com/umccr/sash/issues/19))
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### Changed
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- **Reference data updates:**
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- Updated to hmf_pipeline_resources.38_v2.2.0--3
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- **Process update:**
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- eSVee parameter updates
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- PAVE parameter updates for v1.8 compatibility
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- Updated prepare_input paths for oncoanalyser v2.2.0 structure
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### Removed
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- Unused reference data files (gridss_region_blocklist, lilac, orange, sigs_signatures, disease_ontology)
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### Dependencies
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| Tool | Old | New |
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|------|-----|-----|
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| eSVee | 1.0.3 | 1.1.2 |
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| LINX | 2.0.2 | 2.1 |
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| PAVE | 1.7.1 | 1.8 |
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| PURPLE | 4.1 | 4.2 |
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| bolt | 0.2.14 | 0.2.15 |
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| gpgr | 2.1.3 | 2.2.0 |
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## [0.6.0] - 2025-06-04
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### Added

‎README.md‎

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- PURPLE for TMB, MSI, CNV calling, and purity / ploidy estimation
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- HRDetect and CHORD for HRD inference
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- MutationalPatterns to fit mutational signatures
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- PAVE for somatic variant annotation with MNV filtering (see [discussion](https://github.com/umccr/sash/issues/19))
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## Requirements
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‎conf/refdata.config‎

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data_versions {
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umccr_reference_data = '2--0'
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hmf_reference_data = '5.34_38--2'
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hmf_reference_data = 'hmf_pipeline_resources.38_v2.2.0--3'
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pcgr = '20220203'
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snpeff = '5_1'
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// NOTE(SW): this should be shared with oncoanalyser
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hmfdata_paths {
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// AMBER
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heterozygous_sites = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna_pipeline/copy_number/AmberGermlineSites.38.tsv.gz"
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heterozygous_sites = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna/copy_number/AmberGermlineSites.38.tsv.gz"
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// COBALT
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gc_profile = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna_pipeline/copy_number/GC_profile.1000bp.38.cnp"
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diploid_bed = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna_pipeline/copy_number/DiploidRegions.38.bed.gz"
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gc_profile = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna/copy_number/GC_profile.1000bp.38.cnp"
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diploid_bed = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna/copy_number/DiploidRegions.38.bed.gz"
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// CUPPA
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cuppa_resources = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/cuppa/"
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cuppa_resources = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/misc/cuppa/"
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// SV Prep
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sv_prep_blocklist = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna_pipeline/sv/sv_prep_blacklist.38.bed"
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sv_prep_blocklist = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna/sv/sv_prep_blacklist.38.bed"
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// GRIDSS, GRIPSS
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gridss_pon_breakends = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna_pipeline/sv/sgl_pon.38.bed.gz"
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gridss_pon_breakpoints = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna_pipeline/sv/sv_pon.38.bedpe.gz"
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gridss_region_blocklist = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna_pipeline/sv/gridss_blacklist.38.bed.gz"
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repeatmasker_annotations = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna_pipeline/sv/repeat_mask_data.38.fa.gz"
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gridss_pon_breakends = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna/sv/sgl_pon.38.bed.gz"
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gridss_pon_breakpoints = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna/sv/sv_pon.38.bedpe.gz"
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repeatmasker_annotations = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna/sv/repeat_mask_data.38.fa.gz"
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// Isofox
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isofox_counts = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/rna_pipeline/read_151_exp_counts.csv"
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isofox_gc_ratios = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/rna_pipeline/read_100_exp_gc_ratios.csv"
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// LILAC
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lilac_resources = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna_pipeline/immune/"
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// ORANGE
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cohort_mapping = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/orange/cohort_mapping.tsv"
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cohort_percentiles = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/orange/cohort_percentiles.tsv"
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alt_sj_distribution = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/rna_pipeline/isofox.hmf_3444.alt_sj_cohort.38.csv"
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gene_exp_distribution = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/rna_pipeline/isofox.hmf_3444.gene_distribution.38.csv"
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isofox_counts = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/rna/read_151_exp_counts.38.csv"
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isofox_gc_ratios = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/rna/read_100_exp_gc_ratios.38.csv"
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// SAGE
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clinvar_annotations = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna_pipeline/variants/clinvar.38.vcf.gz"
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sage_blocklist_regions = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna_pipeline/variants/KnownBlacklist.germline.38.bed"
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sage_highconf_regions = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna_pipeline/variants/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_noCENorHET7.bed.gz"
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sage_known_hotspots_somatic = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna_pipeline/variants/KnownHotspots.somatic.38.vcf.gz"
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sage_pon = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna_pipeline/variants/SageGermlinePon.98x.38.tsv.gz"
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// Sigs
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sigs_signatures = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/sigs/snv_cosmic_signatures.csv"
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clinvar_annotations = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna/variants/clinvar.38.vcf.gz"
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sage_blocklist_regions = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna/variants/KnownBlacklist.germline.38.bed"
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sage_highconf_regions = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna/variants/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_noCENorHET7.bed.gz"
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sage_known_hotspots_somatic = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna/variants/KnownHotspots.somatic.38.vcf.gz"
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sage_pon = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna/variants/hmf_wgs_sage_pon_1000.38.tsv.gz"
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// Virus Interpreter
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virus_reporting_db = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/virusinterpreter/virus_reporting_db.tsv"
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virus_taxonomy_db = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/virusinterpreter/taxonomy_db.tsv"
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virus_reporting_db = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/misc/virusinterpreter/virus_reporting_db.tsv"
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virus_taxonomy_db = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/misc/virusinterpreter/taxonomy_db.tsv"
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// Misc
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disease_ontology = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/disease_ontology/doid.json"
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gnomad_resource = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna_pipeline/variants/gnomad/"
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gridss_config = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna_pipeline/sv/gridss.properties"
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purple_germline_del = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna_pipeline/copy_number/cohort_germline_del_freq.38.csv"
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segment_mappability = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna_pipeline/variants/mappability_150.38.bed.gz"
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gnomad_resource = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna/variants/gnomad/"
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gridss_config = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna/sv/gridss.properties"
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purple_germline_del = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna/copy_number/cohort_germline_del_freq.38.csv"
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segment_mappability = "hmf_reference_data/hmftools/${data_versions.hmf_reference_data}/dna/variants/mappability_150.38.bed.gz"
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}
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}

‎modules/local/bolt/other/cancer_report/main.nf‎

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tag "${meta.id}"
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label 'process_low'
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container 'ghcr.io/umccr/bolt:0.2.14-gpgr'
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container 'ghcr.io/umccr/bolt:0.2.15-gpgr'
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input:
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tuple val(meta), path(smlv_somatic_vcf), path(smlv_somatic_bcftools_stats), path(smlv_somatic_counts_process), path(sv_somatic_tsv), path(sv_somatic_vcf), path(cnv_somatic_tsv), path(af_global), path(af_keygenes), path(purple_baf_plot), path(purple_dir), path(virusbreakend_dir), path(dragen_hrd)

‎modules/local/bolt/other/multiqc_report/main.nf‎

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tag "${meta.id}"
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label 'process_low'
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container 'ghcr.io/umccr/bolt:0.2.14-multiqc'
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container 'ghcr.io/umccr/bolt:0.2.15-multiqc'
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tuple val(meta), path(input_files)

‎modules/local/bolt/other/purple_baf_plot/main.nf‎

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tag "${meta.id}"
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container 'ghcr.io/umccr/bolt:0.2.14-circos'
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container 'ghcr.io/umccr/bolt:0.2.15-circos'
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tuple val(meta), path(purple_dir)

‎modules/local/bolt/smlv_germline/prepare/main.nf‎

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container 'ghcr.io/umccr/bolt:0.2.14'
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container 'ghcr.io/umccr/bolt:0.2.15'
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‎modules/local/bolt/smlv_germline/report/main.nf‎

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container 'ghcr.io/umccr/bolt:0.2.14-pcgr'
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container 'ghcr.io/umccr/bolt:0.2.15-pcgr'
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tuple val(meta), path(smlv_vcf), path(smlv_unfiltered_vcf)

‎modules/local/bolt/smlv_somatic/annotate/main.nf‎

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container 'ghcr.io/umccr/bolt:0.2.14-pcgr'
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container 'ghcr.io/umccr/bolt:0.2.15-pcgr'
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tuple val(meta), path(smlv_vcf)

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