add more sage test files

Author: sorelfitzgibbon

test/config/a_mini-sage-skip-redux.config

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+/*
+*      Config file for testing SAGE with REDUX completely skipped
+*       This configuration demonstrates running SAGE directly on original BAM files
+*       without any REDUX preprocessing
+*/
+
+/**
+*       EXECUTION SETTINGS AND GLOBAL DEFAULTS
+*       External config files import. DO NOT MODIFY THESE LINES!
+*/
+includeConfig "${projectDir}/config/default.config"
+includeConfig "${projectDir}/nextflow.config"
+includeConfig "${projectDir}/config/methods.config"
+
+/**
+*       Inputs/parameters of the pipeline
+*/
+
+params {
+    algorithm = ['sage'] // 'somaticsniper', 'strelka2', 'mutect2', 'muse', 'sage'
+    reference = '/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta'
+    reference_version = '38'
+    intersect_regions = '/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz'
+    dataset_id = 'TWGSAMIN'
+    // set params.exome to TRUE will add the '--exome' option when running Manta and Strelka2
+    // set params.exome to TRUE will add the '-E' option when running MuSE
+    exome = false
+    save_intermediate_files = true
+
+    // module options
+    bgzip_extra_args = ''
+    tabix_extra_args = ''
+
+    // mutect2 options
+    split_intervals_extra_args = ''
+    mutect2_extra_args = ''
+    filter_mutect_calls_extra_args = ''
+    gatk_command_mem_diff = 500.MB
+    scatter_count = 50
+    germline_resource_gnomad_vcf = '/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz'
+
+    // MuSE options
+    dbSNP = '/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz'
+
+    // REDUX options
+    redux_additional_args = ''
+    redux_unmap_regions = '/hot/user/sfitzgibbon/hmf_pipeline_resources.38_v2.0--3/common/unmap_regions.38.tsv'
+    redux_ref_genome_msi_file = '/hot/user/sfitzgibbon/hmf_pipeline_resources.38_v2.0--3/dna/variants/msi_jitter_sites.38.tsv.gz'
+    redux_form_consensus = false
+    redux_jitter_msi_only = false
+    redux_skip = true  // This completely skips REDUX processing
+
+    // SAGE options
+    sage_additional_args = ''
+    sage_hotspots = '/hot/user/sfitzgibbon/hmf_pipeline_resources.38_v2.0--3/dna/variants/KnownHotspots.somatic.38.vcf.gz'
+    sage_panel_bed = '/hot/user/sfitzgibbon/hmf_pipeline_resources.38_v2.0--3/dna/variants/ActionableCodingPanel.38.bed.gz'
+    sage_ensembl_data_dir = '/hot/user/sfitzgibbon/hmf_pipeline_resources.38_v2.0--3/common/ensembl_data'
+    sage_high_confidence_bed = '/hot/user/sfitzgibbon/hmf_pipeline_resources.38_v2.0--3/dna/variants/HG001_GRCh38_GIAB_highconf_CG-IllFB-IllGATKHC-Ion-10X-SOLID_CHROM1-X_v.3.3.2_highconf_nosomaticdel_noCENorHET7.bed.gz'
+    sage_command_mem_diff = 3.GB
+    // Note: MSI jitter correction is automatically skipped when redux_skip = true
+
+    // Intersect options
+    vcf2maf_extra_args = ''
+
+    // Base resource allocation updater
+    // See README for adding parameters to update the base resource allocations
+}
+
+// Setup the pipeline config. DO NOT REMOVE THIS LINE!
+methods.setup()

test/yaml/a_mini-jitter.yaml

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+---
+patient_id: 'TWGSAMIN000001'
+input:
+  normal:
+    - BAM: /hot/data/unregistered/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam
+  tumor:
+    - BAM: /hot/data/unregistered/SMC-HET/tumours/A-mini/bams/n2/output/S2.T-n2.bam
+      contamination_table: /hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/input/data/A-mini/S2.T-n2_getpileupsummaries_calculatecontamination.table
+
+# Pre-computed REDUX jitter parameters and MS tables
+# These files will be used instead of running REDUX preprocessing
+redux_provided_ms_table_tumor: '/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-input/S2-v1.1.5.ms_table.tsv.gz'
+redux_provided_ms_table_normal: '/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-input/HG002.N.ms_table.tsv.gz'
+redux_provided_jitter_params_tumor: '/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-input/S2-v1.1.5.jitter_params.tsv'
+redux_provided_jitter_params_normal: '/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/test-input/HG002.N.jitter_params.tsv'