class: Workflow cwlVersion: v1.0 id: tindaisy label: TinDaisy-Hotspot inputs: - id: no_delete_temp type: boolean? - id: tumor_bam type: File - id: normal_bam type: File - id: reference_fasta type: File - id: pindel_config type: File - id: varscan_config type: File - id: pindel_vcf_filter_config type: File - id: dbsnp_db type: File? - id: assembly type: string? - id: vep_cache_version type: string? - id: vep_cache_gz type: File? - id: centromere_bed type: File? - id: strelka_vcf_filter_config type: File - id: varscan_vcf_filter_config type: File - id: af_filter_config type: File - id: classification_filter_config type: File - id: mutect_vcf_filter_config type: File - id: strelka_config type: File - id: chrlist type: File? - id: num_parallel_pindel type: int? - id: num_parallel_strelka2 type: int? - id: tumor_barcode type: string? - id: normal_barcode type: string? - id: Hotspot_BED type: File - id: canonical_BED type: File - id: call_regions type: File? - id: mutect_vcf_filter_config_A type: File - id: pindel_vcf_filter_config_A type: File - id: varscan_vcf_filter_config_A type: File - id: strelka_vcf_filter_config_A type: File outputs: - id: output_maf outputSource: vcf2maf/output type: File? - id: output_vcf outputSource: canonical_filter/output type: File steps: - id: run_pindel in: - id: tumor_bam source: tumor_bam - id: normal_bam source: normal_bam - id: reference_fasta source: reference_fasta - id: centromere_bed source: centromere_bed - id: no_delete_temp source: no_delete_temp - id: pindel_config source: pindel_config - id: chrlist source: chrlist - id: num_parallel_pindel source: num_parallel_pindel out: - id: pindel_raw run: ../tools/run_pindel.cwl label: run_pindel - id: run_varscan in: - id: tumor_bam source: tumor_bam - id: normal_bam source: normal_bam - id: reference_fasta source: reference_fasta - id: varscan_config source: varscan_config out: - id: varscan_indel_raw - id: varscan_snv_raw run: ../tools/run_varscan.cwl label: run_varscan - id: parse_pindel in: - id: pindel_raw source: run_pindel/pindel_raw - id: reference_fasta source: reference_fasta - id: pindel_config source: pindel_config out: - id: pindel_vcf run: ../tools/parse_pindel.cwl label: parse_pindel - id: parse_varscan_snv in: - id: varscan_indel_raw source: run_varscan/varscan_indel_raw - id: varscan_snv_raw source: run_varscan/varscan_snv_raw - id: varscan_config source: varscan_config out: - id: varscan_snv run: ../tools/parse_varscan_snv.cwl label: parse_varscan_snv - id: parse_varscan_indel in: - id: varscan_indel_raw source: run_varscan/varscan_indel_raw - id: varscan_config source: varscan_config out: - id: varscan_indel run: ../tools/parse_varscan_indel.cwl label: parse_varscan_indel - id: merge_vcf in: - id: strelka_snv_vcf source: hotspot_vld_strelka_snv/output - id: varscan_indel_vcf source: hotspot_vld_varscan_indel/output - id: varscan_snv_vcf source: hotspot_vld_varscan_snv/output - id: pindel_vcf source: hotspot_vld_pindel/output - id: reference_fasta source: reference_fasta - id: strelka_indel_vcf source: hotspot_vld_strelka_indel/output - id: mutect_vcf source: hotspot_vld_mutect/output out: - id: merged_vcf run: ../tools/merge_vcf.cwl label: merge_vcf - id: dbsnp_filter in: - id: input_vcf source: mnp_filter/filtered_VCF - id: reference_fasta source: reference_fasta - id: dbsnp_db source: dbsnp_db out: - id: filtered_vcf run: ../tools/dbsnp_filter.cwl label: dbsnp_filter - id: vep_annotate in: - id: input_vcf source: dbsnp_filter/filtered_vcf - id: reference_fasta source: reference_fasta - id: assembly source: assembly - id: vep_cache_version source: vep_cache_version - id: vep_cache_gz source: vep_cache_gz out: - id: output_dat run: ../tools/vep_annotate.cwl label: vep_annotate - id: vep_filter in: - id: input_vcf source: vep_annotate/output_dat - id: af_filter_config source: af_filter_config - id: classification_filter_config source: classification_filter_config out: - id: output_vcf run: ../tools/vep_filter.cwl label: vep_filter - id: mutect in: - id: normal source: normal_bam - id: reference source: reference_fasta - id: tumor source: tumor_bam out: - id: call_stats - id: coverage - id: mutations run: ../mutect-tool/cwl/mutect.cwl label: MuTect - id: run_strelka2 in: - id: tumor_bam source: tumor_bam - id: normal_bam source: normal_bam - id: reference_fasta source: reference_fasta - id: strelka_config source: strelka_config - id: call_regions source: call_regions - id: num_parallel_strelka2 source: num_parallel_strelka2 out: - id: strelka2_snv_vcf - id: strelka2_indel_vcf run: ../tools/run_strelka2.cwl label: run_strelka2 - id: mnp_filter in: - id: input source: merge_vcf/merged_vcf - id: tumor_bam source: tumor_bam out: - id: filtered_VCF run: ../mnp_filter/cwl/mnp_filter.cwl label: MNP_filter - id: vcf2maf in: - id: ref-fasta source: reference_fasta - id: assembly source: assembly - id: input-vcf source: canonical_filter/output - id: tumor_barcode source: tumor_barcode - id: normal_barcode source: normal_barcode out: - id: output run: ../tools/vcf2maf.cwl label: vcf2maf - id: varscan_indel_vcf_remap in: - id: input source: parse_varscan_indel/varscan_indel out: - id: remapped_VCF run: ../varscan_vcf_remap/varscan_vcf_remap.cwl label: varscan_indel_vcf_remap - id: varscan_snv_vcf_remap in: - id: input source: parse_varscan_snv/varscan_snv out: - id: remapped_VCF run: ../varscan_vcf_remap/varscan_vcf_remap.cwl label: varscan_snv_vcf_remap - id: canonical_filter in: - id: VCF_A source: vep_filter/output_vcf - id: BED source: canonical_BED out: - id: output run: ../hotspot_filter/hotspotfilter.cwl label: CanonicalFilter - id: hotspot_vld_mutect in: - id: vcf_filter_config_A source: mutect_vcf_filter_config_A - id: input_vcf source: mutect/mutations - id: vcf_filter_config_B source: mutect_vcf_filter_config - id: BED source: Hotspot_BED out: - id: output run: ./hotspot_vld.cwl label: hotspot_vld_mutect - id: hotspot_vld_pindel in: - id: vcf_filter_config_A source: pindel_vcf_filter_config_A - id: input_vcf source: parse_pindel/pindel_vcf - id: vcf_filter_config_B source: pindel_vcf_filter_config - id: BED source: Hotspot_BED out: - id: output run: ./hotspot_vld.cwl label: hotspot_vld_pindel - id: hotspot_vld_varscan_snv in: - id: vcf_filter_config_A source: varscan_vcf_filter_config_A - id: input_vcf source: varscan_snv_vcf_remap/remapped_VCF - id: vcf_filter_config_B source: varscan_vcf_filter_config - id: BED source: Hotspot_BED out: - id: output run: ./hotspot_vld.cwl label: hotspot_vld_varscan_snv - id: hotspot_vld_varscan_indel in: - id: vcf_filter_config_A source: varscan_vcf_filter_config_A - id: input_vcf source: varscan_indel_vcf_remap/remapped_VCF - id: vcf_filter_config_B source: varscan_vcf_filter_config - id: BED source: Hotspot_BED out: - id: output run: ./hotspot_vld.cwl label: hotspot_vld_varscan_indel - id: hotspot_vld_strelka_snv in: - id: vcf_filter_config_A source: strelka_vcf_filter_config_A - id: input_vcf source: run_strelka2/strelka2_snv_vcf - id: vcf_filter_config_B source: strelka_vcf_filter_config - id: BED source: Hotspot_BED out: - id: output run: ./hotspot_vld.cwl label: hotspot_vld_strelka_snv - id: hotspot_vld_strelka_indel in: - id: vcf_filter_config_A source: strelka_vcf_filter_config_A - id: input_vcf source: run_strelka2/strelka2_indel_vcf - id: vcf_filter_config_B source: strelka_vcf_filter_config - id: BED source: Hotspot_BED out: - id: output run: ./hotspot_vld.cwl label: hotspot_vld_strelka_indel requirements: - class: SubworkflowFeatureRequirement