{"@id":"https://w3id.org/cwl/view/git/f83b0e3d2ab7a29a0425bf25b5bae68c3dc70999/genomel/genomel_cohort_freebayes.cwl","retrievedFrom":{"repoUrl":"https://github.com/uc-cdis/genomel_pipelines.git","branch":"f83b0e3d2ab7a29a0425bf25b5bae68c3dc70999","path":"genomel/genomel_cohort_freebayes.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/uc-cdis/genomel_pipelines/f83b0e3d2ab7a29a0425bf25b5bae68c3dc70999/genomel/genomel_cohort_freebayes.cwl","url":"https://github.com/uc-cdis/genomel_pipelines/blob/f83b0e3d2ab7a29a0425bf25b5bae68c3dc70999/genomel/genomel_cohort_freebayes.cwl"},"retrievedOn":"2026-10-27T00:18:52.309+00:00","lastCommit":"f83b0e3d2ab7a29a0425bf25b5bae68c3dc70999","label":"genomel_cohort_freebayes.cwl","inputs":{"bam":{"type":"File"},"job_uuid":{"type":"String"},"bed_files":{"type":"File[]"},"reference":{"type":"File"},"aws_config":{"type":"File"},"cromwell_engine":{"type":"Boolean"},"upload_s3_bucket":{"type":"String"},"upload_s3_profile":{"type":"String"},"upload_s3_endpoint":{"type":"String"},"aws_shared_credentials":{"type":"File"},"freebayes_thread_count":{"type":"Integer"},"number_of_chunks_for_freebayes":{"type":"Integer"}},"outputs":{"time_logs":{"type":"File[]"},"passed_bed":{"type":"File"},"freebayes_vcf":{"type":"File"}},"steps":{"sort_freebayes":{"run":"cwl/tools/variant_calling/picard_sortvcf.cwl","runType":"COMMANDLINETOOL","sources":{"sort_freebayes":{"sourceIDs":["freebayes_cohort_genotyping"]},"https://w3id.org/cwl/view/git/f83b0e3d2ab7a29a0425bf25b5bae68c3dc70999/genomel/genomel_cohort_freebayes.cwl#sort_freebayes/job_uuid":{"sourceIDs":["job_uuid"]},"https://w3id.org/cwl/view/git/f83b0e3d2ab7a29a0425bf25b5bae68c3dc70999/genomel/genomel_cohort_freebayes.cwl#sort_freebayes/reference_dict":{"sourceIDs":["reference"]}}},"extract_time_log":{"run":"cwl/tools/utils/extract_outputs.cwl","runType":"EXPRESSIONTOOL","sources":{"extract_time_log":{"sourceIDs":["freebayes_cohort_genotyping"]},"https://w3id.org/cwl/view/git/f83b0e3d2ab7a29a0425bf25b5bae68c3dc70999/genomel/genomel_cohort_freebayes.cwl#extract_time_log/file_array":{"sourceIDs":["upload_freebayes_vcf_index"]}}},"merge_passed_bed":{"run":"cwl/tools/utils/merge_files.cwl","runType":"COMMANDLINETOOL","sources":{"merge_passed_bed":{"sourceIDs":["job_uuid"]},"https://w3id.org/cwl/view/git/f83b0e3d2ab7a29a0425bf25b5bae68c3dc70999/genomel/genomel_cohort_freebayes.cwl#merge_passed_bed/input_files":{"sourceIDs":["freebayes_cohort_genotyping"]}}},"upload_passed_bed":{"run":"cwl/tools/utils/awscli_upload.cwl","runType":"COMMANDLINETOOL","sources":{"upload_passed_bed":{"sourceIDs":["merge_passed_bed"]},"https://w3id.org/cwl/view/git/f83b0e3d2ab7a29a0425bf25b5bae68c3dc70999/genomel/genomel_cohort_freebayes.cwl#upload_passed_bed/s3uri":{"sourceIDs":["merge_passed_bed"]},"https://w3id.org/cwl/view/git/f83b0e3d2ab7a29a0425bf25b5bae68c3dc70999/genomel/genomel_cohort_freebayes.cwl#upload_passed_bed/aws_config":{"sourceIDs":["aws_config"]},"https://w3id.org/cwl/view/git/f83b0e3d2ab7a29a0425bf25b5bae68c3dc70999/genomel/genomel_cohort_freebayes.cwl#upload_passed_bed/s3_profile":{"sourceIDs":["upload_s3_profile"]},"https://w3id.org/cwl/view/git/f83b0e3d2ab7a29a0425bf25b5bae68c3dc70999/genomel/genomel_cohort_freebayes.cwl#upload_passed_bed/s3_endpoint":{"sourceIDs":["upload_s3_endpoint"]},"https://w3id.org/cwl/view/git/f83b0e3d2ab7a29a0425bf25b5bae68c3dc70999/genomel/genomel_cohort_freebayes.cwl#upload_passed_bed/aws_shared_credentials":{"sourceIDs":["aws_shared_credentials"]}}},"upload_freebayes_vcf":{"run":"cwl/tools/utils/awscli_upload.cwl","runType":"COMMANDLINETOOL","sources":{"upload_freebayes_vcf":{"sourceIDs":["sort_freebayes"]},"https://w3id.org/cwl/view/git/f83b0e3d2ab7a29a0425bf25b5bae68c3dc70999/genomel/genomel_cohort_freebayes.cwl#upload_freebayes_vcf/s3uri":{"sourceIDs":["upload_s3_bucket"]},"https://w3id.org/cwl/view/git/f83b0e3d2ab7a29a0425bf25b5bae68c3dc70999/genomel/genomel_cohort_freebayes.cwl#upload_freebayes_vcf/aws_config":{"sourceIDs":["aws_config"]},"https://w3id.org/cwl/view/git/f83b0e3d2ab7a29a0425bf25b5bae68c3dc70999/genomel/genomel_cohort_freebayes.cwl#upload_freebayes_vcf/s3_profile":{"sourceIDs":["upload_s3_profile"]},"https://w3id.org/cwl/view/git/f83b0e3d2ab7a29a0425bf25b5bae68c3dc70999/genomel/genomel_cohort_freebayes.cwl#upload_freebayes_vcf/s3_endpoint":{"sourceIDs":["upload_s3_endpoint"]},"https://w3id.org/cwl/view/git/f83b0e3d2ab7a29a0425bf25b5bae68c3dc70999/genomel/genomel_cohort_freebayes.cwl#upload_freebayes_vcf/aws_shared_credentials":{"sourceIDs":["aws_shared_credentials"]}}},"upload_freebayes_vcf_index":{"run":"cwl/tools/utils/awscli_upload.cwl","runType":"COMMANDLINETOOL","sources":{"upload_freebayes_vcf_index":{"sourceIDs":["aws_shared_credentials"]},"https://w3id.org/cwl/view/git/f83b0e3d2ab7a29a0425bf25b5bae68c3dc70999/genomel/genomel_cohort_freebayes.cwl#upload_freebayes_vcf_index/input":{"sourceIDs":["sort_freebayes"]},"https://w3id.org/cwl/view/git/f83b0e3d2ab7a29a0425bf25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