Workflow: genomel_cohort_freebayes.cwl

Fetched 2023-01-09 02:33:00 GMT
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workflow cluster_inputs Workflow Inputs cluster_outputs Workflow Outputs upload_s3_bucket upload_s3_bucket upload_freebayes_vcf_index upload_freebayes_vcf_index upload_s3_bucket->upload_freebayes_vcf_index s3uri upload_freebayes_vcf upload_freebayes_vcf upload_s3_bucket->upload_freebayes_vcf s3uri upload_s3_profile upload_s3_profile upload_s3_profile->upload_freebayes_vcf_index s3_profile upload_s3_profile->upload_freebayes_vcf s3_profile aws_shared_credentials aws_shared_credentials aws_shared_credentials->upload_freebayes_vcf_index aws_shared_credentials aws_shared_credentials->upload_freebayes_vcf aws_shared_credentials reference reference sort_freebayes sort_freebayes reference->sort_freebayes reference_dict freebayes_cohort_genotyping freebayes_cohort_genotyping reference->freebayes_cohort_genotyping reference job_uuid job_uuid job_uuid->sort_freebayes job_uuid job_uuid->freebayes_cohort_genotyping job_uuid bed_files bed_files bed_files->freebayes_cohort_genotyping output_prefix bed_files->freebayes_cohort_genotyping bed_file upload_s3_endpoint upload_s3_endpoint upload_s3_endpoint->upload_freebayes_vcf_index s3_endpoint upload_s3_endpoint->upload_freebayes_vcf s3_endpoint bam bam bam->freebayes_cohort_genotyping bam cromwell_engine cromwell_engine freebayes_thread_count freebayes_thread_count freebayes_thread_count->freebayes_cohort_genotyping thread_count number_of_chunks_for_freebayes number_of_chunks_for_freebayes number_of_chunks_for_freebayes->freebayes_cohort_genotyping number_of_chunks aws_config aws_config aws_config->upload_freebayes_vcf_index aws_config aws_config->upload_freebayes_vcf aws_config freebayes_vcf freebayes_vcf time_logs time_logs sort_freebayes->freebayes_vcf extract_time_log extract_time_log sort_freebayes->extract_time_log file_array sort_freebayes->upload_freebayes_vcf_index s3uri sort_freebayes->upload_freebayes_vcf_index input sort_freebayes->upload_freebayes_vcf s3uri sort_freebayes->upload_freebayes_vcf input extract_time_log->time_logs upload_freebayes_vcf_index->extract_time_log file_array freebayes_cohort_genotyping->sort_freebayes vcf freebayes_cohort_genotyping->extract_time_log file_array freebayes_cohort_genotyping->extract_time_log file_array freebayes_cohort_genotyping->extract_time_log file_array upload_freebayes_vcf->extract_time_log file_array
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Inputs

ID Type Title Doc
bam File
job_uuid String
bed_files File[]
reference File
aws_config File
cromwell_engine Boolean
upload_s3_bucket String
upload_s3_profile String
upload_s3_endpoint String
aws_shared_credentials File
freebayes_thread_count Integer
number_of_chunks_for_freebayes Integer

Steps

ID Runs Label Doc
sort_freebayes
cwl/tools/variant_calling/picard_sortvcf.cwl (CommandLineTool)
extract_time_log
cwl/tools/utils/extract_outputs.cwl (ExpressionTool)
upload_freebayes_vcf
cwl/tools/utils/awscli_upload.cwl (CommandLineTool)
upload_freebayes_vcf_index
cwl/tools/utils/awscli_upload.cwl (CommandLineTool)
freebayes_cohort_genotyping

Outputs

ID Type Label Doc
time_logs File[]
freebayes_vcf File
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