Workflow: genomel_individual_workflow.cwl

Fetched 2023-01-04 17:24:05 GMT
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Inputs

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

Steps

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

Outputs

ID Type Label Doc
time_logs File[]
genomel_bam File
genomel_gvcf File
Permalink: https://w3id.org/cwl/view/git/7f01768479e6a77a5caf6b3382174aa038ba05fc/genomel/genomel_individual_workflow.cwl