#!/usr/bin/env cwl-runner cwlVersion: v1.0 class: Workflow requirements: - class: InlineJavascriptRequirement - class: StepInputExpressionRequirement - class: SubworkflowFeatureRequirement inputs: - id: gdc_token type: File - id: input_bam_gdc_id type: string - id: input_bam_file_size type: long - id: known_snp_gdc_id type: string - id: known_snp_file_size type: long - id: known_snp_index_gdc_id type: string - id: known_snp_index_file_size type: long - id: reference_amb_gdc_id type: string - id: reference_amb_file_size type: long - id: reference_ann_gdc_id type: string - id: reference_ann_file_size type: long - id: reference_bwt_gdc_id type: string - id: reference_bwt_file_size type: long - id: reference_dict_gdc_id type: string - id: reference_dict_file_size type: long - id: reference_fa_gdc_id type: string - id: reference_fa_file_size type: long - id: reference_fai_gdc_id type: string - id: reference_fai_file_size type: long - id: reference_pac_gdc_id type: string - id: reference_pac_file_size type: long - id: reference_sa_gdc_id type: string - id: reference_sa_file_size type: long - id: thread_count type: long - id: job_uuid type: string outputs: - id: bam type: File outputSource: transform/bam - id: sqlite type: File outputSource: transform/sqlite steps: - id: extract_bam run: ../../tools/gdc_get_object.cwl in: - id: gdc_token source: gdc_token - id: gdc_uuid source: input_bam_gdc_id - id: file_size source: input_bam_file_size out: - id: output - id: extract_known_snp run: ../../tools/gdc_get_object.cwl in: - id: gdc_token source: gdc_token - id: gdc_uuid source: known_snp_gdc_id - id: file_size source: known_snp_file_size out: - id: output - id: extract_known_snp_index run: ../../tools/gdc_get_object.cwl in: - id: gdc_token source: gdc_token - id: gdc_uuid source: known_snp_index_gdc_id - id: file_size source: known_snp_index_file_size out: - id: output - id: extract_reference_amb run: ../../tools/gdc_get_object.cwl in: - id: gdc_token source: gdc_token - id: gdc_uuid source: reference_amb_gdc_id - id: file_size source: reference_amb_file_size out: - id: output - id: extract_reference_ann run: ../../tools/gdc_get_object.cwl in: - id: gdc_token source: gdc_token - id: gdc_uuid source: reference_ann_gdc_id - id: file_size source: reference_ann_file_size out: - id: output - id: extract_reference_bwt run: ../../tools/gdc_get_object.cwl in: - id: gdc_token source: gdc_token - id: gdc_uuid source: reference_bwt_gdc_id - id: file_size source: reference_bwt_file_size out: - id: output - id: extract_reference_dict run: ../../tools/gdc_get_object.cwl in: - id: gdc_token source: gdc_token - id: gdc_uuid source: reference_dict_gdc_id - id: file_size source: reference_dict_file_size out: - id: output - id: extract_reference_fa run: ../../tools/gdc_get_object.cwl in: - id: gdc_token source: gdc_token - id: gdc_uuid source: reference_fa_gdc_id - id: file_size source: reference_fa_file_size out: - id: output - id: extract_reference_fai run: ../../tools/gdc_get_object.cwl in: - id: gdc_token source: gdc_token - id: gdc_uuid source: reference_fai_gdc_id - id: file_size source: reference_fai_file_size out: - id: output - id: extract_reference_pac run: ../../tools/gdc_get_object.cwl in: - id: gdc_token source: gdc_token - id: gdc_uuid source: reference_pac_gdc_id - id: file_size source: reference_pac_file_size out: - id: output - id: extract_reference_sa run: ../../tools/gdc_get_object.cwl in: - id: gdc_token source: gdc_token - id: gdc_uuid source: reference_sa_gdc_id - id: file_size source: reference_sa_file_size out: - id: output - id: root_fasta_files run: ../../tools/root_fasta_dnaseq.cwl in: - id: fasta source: extract_reference_fa/output - id: fasta_amb source: extract_reference_amb/output - id: fasta_ann source: extract_reference_ann/output - id: fasta_bwt source: extract_reference_bwt/output - id: fasta_dict source: extract_reference_dict/output - id: fasta_fai source: extract_reference_fai/output - id: fasta_pac source: extract_reference_pac/output - id: fasta_sa source: extract_reference_sa/output out: - id: output - id: root_known_snp_files run: ../../tools/root_vcf.cwl in: - id: vcf source: extract_known_snp/output - id: vcf_index source: extract_known_snp_index/output out: - id: output - id: transform run: transform.cwl in: - id: input_bam source: extract_bam/output - id: known_snp source: root_known_snp_files/output - id: reference_sequence source: root_fasta_files/output - id: thread_count source: thread_count - id: job_uuid source: job_uuid out: - id: bam - id: sqlite