Workflow: genomel_individual_workflow.cwl

Fetched 2019-05-20 23:20:35 GMT
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Inputs

ID Type Title Doc
job_uuid String
known_snp File
fastq_read1_md5 String[]
aws_shared_credentials File
exome_bed File
input_is_fastq Integer[]
fastq_read1_uri String[]
bam_uri String
readgroup_lines String[]
upload_s3_endpoint String
reference File
fastq_read2_md5 String[]
readgroup_names String[]
download_s3_profile String
bam_md5 String
fastq_read2_uri String[]
upload_s3_profile String
download_s3_endpoint String
aws_config File
input_is_bam Integer[]
upload_s3_bucket String

Steps

ID Runs Label Doc
gatk3_haplotypecaller
extract_genomel_bam
cwl/tools/utils/extract_genomel_bam.cwl (ExpressionTool)
fastq_input_alignment_with_bwa
extract_bam
cwl/tools/utils/extract_outputs.cwl (ExpressionTool)
bam_input_harmonization_with_bwa
upload_results
extract_time_log
cwl/tools/utils/extract_outputs.cwl (ExpressionTool)
download_fastq_reads
download_bam_file

Outputs

ID Type Label Doc
genomel_bam File
genomel_gvcf File
time_logs File[]
Permalink: https://w3id.org/cwl/view/git/7504ead048c3acd64b9b92e44d044d558cb696f2/genomel/genomel_individual_workflow.cwl