diff --git a/workflows/kfdrc_controlfreec_tumor_only_wf.cwl b/workflows/kfdrc_controlfreec_tumor_only_wf.cwl deleted file mode 100644 index 348ae56..0000000 --- a/workflows/kfdrc_controlfreec_tumor_only_wf.cwl +++ /dev/null @@ -1,127 +0,0 @@ -cwlVersion: v1.2 -class: Workflow -id: kfdrc_controlfreec_tumor_only_wf -requirements: - - class: ScatterFeatureRequirement - - class: MultipleInputFeatureRequirement - - class: SubworkflowFeatureRequirement -inputs: - # Required - reference_fasta: { type: File } - reference_fai: {type: File } - reference_dict: {type: 'File?'} - input_tumor_aligned: {type: "File", secondaryFiles: ["^.bai?", ".bai?", "^.crai?", ".crai?"], doc: "Input bam / cram file"} - input_tumor_name: string - - mate_copynumber_file_sample: {type: 'File?', doc: "Tumor cpn file from previous run. If used, will override bam use"} - gem_mappability_file: {type: 'File?', doc: "GEM mappability file to make read count adjustments with"} - min_subclone_presence: {type: 'float?', doc: "Use if you want to detect subclones. Recommend 0.2 for WGS, 0.3 for WXS"} - cfree_chr_len: { type: File, doc: "file with chromosome lengths" } - cfree_ploidy: { type: 'int[]', doc: "Array of ploidy possibilities for ControlFreeC to try" } - output_basename: { type: string, doc: "String value to use as basename for outputs" } - wgs_or_wxs: { type: { type: enum, name: exp_type, symbols: ["WGS", "WXS"] }, doc: "Select if this run is WGS or WXS" } - - # Optional with One Default - cfree_threads: { type: 'int?', default: 16, doc: "For ControlFreeC. Recommend 16 max, as I/O gets saturated after that losing any advantage" } - cfree_mate_orientation_sample: { type: ['null', { type: enum, name: mate_orientation_sample, symbols: ["0", "FR", "RF", "FF"] }], default: "FR", doc: "0 (for single ends), RF (Illumina mate-pairs), FR (Illumina paired-ends), FF (SOLiD mate-pairs)" } - - # Optional with Multiple Defaults (handled in choose_defaults) - i_flag: { type: 'string?', doc: "Flag to intersect germline calls on padded regions. Use N if you want to skip this or have a WGS run" } - - # Optional - b_allele: { type: 'File?', doc: "germline calls, needed for BAF. GATK HC VQSR input recommended. Tool will prefilter for germline and pass if expression given" } - b_allele_index: { type: 'File?', doc: "Tabix index for b_allele" } - cfree_coeff_var: { type: 'float?', default: 0.05, doc: "Coefficient of variation to set window size. Default 0.05 recommended" } - cfree_sex: { type: ['null', { type: enum, name: sex, symbols: ["XX", "XY"] }], doc: "If known, XX for female, XY for male" } - - # WXS only Fields - unpadded_capture_regions: { type: 'File?', doc: "Capture regions with NO padding for cnv calling" } - -outputs: - ctrlfreec_cnvs: {type: File, outputSource: run_controlfreec/ctrlfreec_cnvs} - ctrlfreec_pval: { type: File, outputSource: run_controlfreec/ctrlfreec_pval } - ctrlfreec_config: { type: File, outputSource: run_controlfreec/ctrlfreec_config } - ctrlfreec_pngs: { type: 'File[]', outputSource: run_controlfreec/ctrlfreec_pngs } - ctrlfreec_bam_ratio: { type: File, outputSource: run_controlfreec/ctrlfreec_bam_ratio } - ctrlfreec_bam_seg: { type: File, outputSource: run_controlfreec/ctrlfreec_bam_seg } - ctrlfreec_baf: { type: File, outputSource: run_controlfreec/ctrlfreec_baf } - ctrlfreec_info: { type: File, outputSource: run_controlfreec/ctrlfreec_info } - -steps: - choose_defaults: - run: ../tools/mode_defaults.cwl - in: - input_mode: wgs_or_wxs - i_flag: i_flag - out: [out_exome_flag, out_cnvkit_wgs_mode, out_i_flag,out_lancet_padding, out_lancet_window, out_vardict_padding] - - prepare_reference: - run: ../subworkflows/prepare_reference.cwl - in: - input_fasta: reference_fasta - input_fai: reference_fai - input_dict: reference_dict - out: [indexed_fasta,reference_dict] - - index_b_allele: - run: ../tools/tabix_index.cwl - in: - input_file: b_allele - input_index: b_allele_index - out: [output] - - bedtools_intersect_germline: - run: ../tools/bedtools_intersect.cwl - in: - input_vcf: index_b_allele/output - output_basename: output_basename - input_bed_file: unpadded_capture_regions - flag: choose_defaults/out_i_flag - out: - [intersected_vcf] - - gatk_filter_germline: - run: ../tools/gatk_filter_germline_variant.cwl - in: - input_vcf: bedtools_intersect_germline/intersected_vcf - reference_fasta: prepare_reference/indexed_fasta - output_basename: output_basename - out: - [filtered_vcf, filtered_pass_vcf] - - samtools_cram2bam_plus_calmd_tumor: - run: ../tools/samtools_calmd.cwl - in: - input_reads: input_tumor_aligned - threads: - valueFrom: ${return 16;} - reference: prepare_reference/indexed_fasta - out: [bam_file] - - run_controlfreec: - run: ../subworkflows/kfdrc_controlfreec_sub_wf.cwl - in: - mate_copynumber_file_sample: mate_copynumber_file_sample - gem_mappability_file: gem_mappability_file - min_subclone_presence: min_subclone_presence - input_tumor_aligned: samtools_cram2bam_plus_calmd_tumor/bam_file - input_tumor_name: input_tumor_name - threads: cfree_threads - output_basename: output_basename - ploidy: cfree_ploidy - mate_orientation_sample: cfree_mate_orientation_sample - capture_regions: unpadded_capture_regions - indexed_reference_fasta: prepare_reference/indexed_fasta - reference_fai: reference_fai - b_allele: gatk_filter_germline/filtered_pass_vcf - chr_len: cfree_chr_len - coeff_var: cfree_coeff_var - cfree_sex: cfree_sex - out: - [ctrlfreec_cnvs, ctrlfreec_pval, ctrlfreec_config, ctrlfreec_pngs, ctrlfreec_bam_ratio, ctrlfreec_bam_seg, ctrlfreec_baf, ctrlfreec_info] - -$namespaces: - sbg: https://sevenbridges.com -hints: - - class: 'sbg:maxNumberOfParallelInstances' - value: 4 diff --git a/workflows/kfdrc_production_manta_wf.cwl b/workflows/kfdrc_production_manta_wf.cwl deleted file mode 100644 index 8b458c5..0000000 --- a/workflows/kfdrc_production_manta_wf.cwl +++ /dev/null @@ -1,62 +0,0 @@ -cwlVersion: v1.2 -class: Workflow -id: kfdrc_production_manta_wf -requirements: - - class: ScatterFeatureRequirement - - class: MultipleInputFeatureRequirement - - class: SubworkflowFeatureRequirement -inputs: - # Required - reference_fasta: { type: File } - reference_fai: { type: 'File?' } - reference_dict: { type: 'File?' } - input_tumor_aligned: { type: File, secondaryFiles: ["^.bai?", ".bai?", "^.crai?", ".crai?"], doc: "tumor BAM or CRAM" } - input_tumor_name: string - hg38_strelka_bed: { type: File, doc: "Bgzipped interval bed file. Recommned padding 100bp for WXS; Recommend canonical chromosomes for WGS" } - hg38_strelka_tbi: { type: 'File?', doc: "Tabix index for hg38_strelka_bed" } - output_basename: { type: string, doc: "String value to use as basename for outputs" } - - # Optional with One Default - select_vars_mode: { type: ['null', { type: enum, name: select_vars_mode, symbols: ["gatk", "grep"] }], default: "gatk", doc: "Choose 'gatk' for SelectVariants tool, or 'grep' for grep expression" } - manta_memory: {type: 'int?', doc: "GB of memory to allocate to Manta; defaults to 10 (soft-capped)"} - manta_cores: {type: 'int?', doc: "Number of cores to allocate to Manta; defaults to 18"} - -outputs: - manta_pass_vcf: { type: File, outputSource: run_manta/manta_pass_vcf } - manta_prepass_vcf: { type: File, outputSource: run_manta/manta_prepass_vcf } - manta_small_indels: { type: File, outputSource: run_manta/manta_small_indels } - -steps: - prepare_reference: - run: ../subworkflows/prepare_reference.cwl - in: - input_fasta: reference_fasta - input_fai: reference_fai - input_dict: reference_dict - out: [indexed_fasta,reference_dict] - - index_strelka_bed: - run: ../tools/tabix_index.cwl - in: - input_file: hg38_strelka_bed - input_index: hg38_strelka_tbi - out: [output] - - run_manta: - run: ../subworkflows/kfdrc_manta_sub_wf.cwl - in: - indexed_reference_fasta: prepare_reference/indexed_fasta - hg38_strelka_bed: index_strelka_bed/output - input_tumor_aligned: input_tumor_aligned - input_tumor_name: input_tumor_name - output_basename: output_basename - manta_memory: manta_memory - manta_cores: manta_cores - out: - [manta_prepass_vcf, manta_pass_vcf, manta_small_indels] - -$namespaces: - sbg: https://sevenbridges.com -hints: - - class: 'sbg:maxNumberOfParallelInstances' - value: 2