Workflow: genomel_cohort_genotyping.cwl

Fetched 2019-05-20 22:43:18 GMT
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Inputs

ID Type Title Doc
job_uuid String
aws_shared_credentials File
freebayes_thread_count Integer
upload_s3_endpoint String
number_of_chunks_for_gatk Integer
reference File
bam_files File[]
number_of_chunks_for_freebayes Integer
gvcf_files File[]
cromwell_engine Boolean
bed_files File[]
gatk4_genotyping_thread_count Integer
upload_s3_profile String
aws_config File
upload_s3_bucket String

Steps

ID Runs Label Doc
sort_ensemble
cwl/tools/variant_calling/picard_sortvcf.cwl (CommandLineTool)
sort_freebayes
cwl/tools/variant_calling/picard_sortvcf.cwl (CommandLineTool)
upload_gatk4_vcf
cwl/tools/utils/awscli_upload.cwl (CommandLineTool)
freebayes_cohort_genotyping
upload_ensemble_vcf
cwl/tools/utils/awscli_upload.cwl (CommandLineTool)
variant_ensemble
cwl/tools/variant_calling/vArmyKnife_variant_ensemble.cwl (CommandLineTool)
upload_freebayes_vcf
cwl/tools/utils/awscli_upload.cwl (CommandLineTool)
extract_time_log
cwl/tools/utils/extract_outputs.cwl (ExpressionTool)
gatk4_cohort_genotyping
upload_freebayes_vcf_index
cwl/tools/utils/awscli_upload.cwl (CommandLineTool)
upload_gatk4_vcf_index
cwl/tools/utils/awscli_upload.cwl (CommandLineTool)
sort_gatk4
cwl/tools/variant_calling/picard_sortvcf.cwl (CommandLineTool)
upload_ensemble_vcf_index
cwl/tools/utils/awscli_upload.cwl (CommandLineTool)

Outputs

ID Type Label Doc
gatk4_vcf File
freebayes_vcf File
variant_ensemble_vcf File
time_logs File[]
Permalink: https://w3id.org/cwl/view/git/7504ead048c3acd64b9b92e44d044d558cb696f2/genomel/genomel_cohort_genotyping.cwl