CWL Workflow: genomel_individual_workflow.cwl

This workflow is Open Source and may be reused according to the terms of: Apache License 2.0

Note that the tools invoked by the workflow may have separate licenses.

Inputs

ID	Type	Title	Doc
bam_uri	String
job_uuid	String
known_snp	File
reference	File
aws_config	File
input_is_bam	Integer[]
known_indel1	File
known_indel2	File
input_is_fastq	Integer[]
fastq_read1_uri	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
run_gatk3_realignment	Integer[]
aws_shared_credentials	File

ID	Runs	Label	Doc
extract_bam	cwl/tools/utils/extract_outputs.cwl (ExpressionTool)
get_fai_bed	cwl/tools/harmonization/fai_to_bed.cwl (CommandLineTool)
upload_results	cwl/workflows/utils/upload_results.cwl (Workflow)
extract_time_log	cwl/tools/utils/extract_outputs.cwl (ExpressionTool)
download_bam_file	cwl/tools/utils/awscli_download.cwl (CommandLineTool)
gatk3_realignment	cwl/workflows/realignment/gatk3_realignment.cwl (Workflow)
extract_genomel_bam	cwl/tools/utils/extract_genomel_bam.cwl (ExpressionTool)
download_fastq_reads	cwl/workflows/utils/download_prep.cwl (Workflow)
gatk3_haplotypecaller	cwl/workflows/variant_calling/haplotypecaller.cwl (Workflow)
fastq_input_alignment_with_bwa	cwl/workflows/harmonization/alignment_bwa_mem.cwl (Workflow)
bam_input_harmonization_with_bwa	cwl/workflows/harmonization/harmonization_bwa_mem.cwl (Workflow)

ID	Type	Label	Doc
time_logs	File[]
genomel_bam	File
genomel_gvcf	File