CWL Workflow: etl.cwl

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Inputs/Outputs

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Inputs

ID	Type	Title	Doc
uuid	String
aws_config	File
load_bucket	String
start_token	File
db_cred_path	File
thread_count	Integer
endpoint_json	File
bam_signpost_id	String
signpost_base_url	String
db_snp_signpost_id	String
load_s3cfg_section	String
aws_shared_credentials	File
reference_fa_signpost_id	String
reference_sa_signpost_id	String
reference_amb_signpost_id	String
reference_ann_signpost_id	String
reference_bwt_signpost_id	String
reference_fai_signpost_id	String
reference_pac_signpost_id	String

Steps

ID	Runs	Label	Doc
load_bai	../../tools/aws_s3_put.cwl (CommandLineTool)
load_bam	../../tools/aws_s3_put.cwl (CommandLineTool)
transform	transform.cwl (Workflow)
extract_bam	../../tools/aws_s3_get_signpost.cwl (CommandLineTool)
load_sqlite	../../tools/aws_s3_put.cwl (CommandLineTool)
extract_db_snp	../../tools/aws_s3_get_signpost.cwl (CommandLineTool)
extract_ref_fa	../../tools/aws_s3_get_signpost.cwl (CommandLineTool)
extract_ref_sa	../../tools/aws_s3_get_signpost.cwl (CommandLineTool)
generate_token	../../tools/generate_load_token.cwl (CommandLineTool)
extract_ref_amb	../../tools/aws_s3_get_signpost.cwl (CommandLineTool)
extract_ref_ann	../../tools/aws_s3_get_signpost.cwl (CommandLineTool)
extract_ref_bwt	../../tools/aws_s3_get_signpost.cwl (CommandLineTool)
extract_ref_fai	../../tools/aws_s3_get_signpost.cwl (CommandLineTool)
extract_ref_pac	../../tools/aws_s3_get_signpost.cwl (CommandLineTool)
root_fasta_files	../../tools/copy_files_to_dir.cwl (CommandLineTool)
extract_bam_signpost	../../tools/get_signpost_json.cwl (CommandLineTool)
generate_s3load_path	../../tools/generate_s3load_path.cwl (ExpressionTool)
extract_db_snp_signpost	../../tools/get_signpost_json.cwl (CommandLineTool)
extract_ref_fa_signpost	../../tools/get_signpost_json.cwl (CommandLineTool)
extract_ref_sa_signpost	../../tools/get_signpost_json.cwl (CommandLineTool)
extract_ref_amb_signpost	../../tools/get_signpost_json.cwl (CommandLineTool)
extract_ref_ann_signpost	../../tools/get_signpost_json.cwl (CommandLineTool)
extract_ref_bwt_signpost	../../tools/get_signpost_json.cwl (CommandLineTool)
extract_ref_fai_signpost	../../tools/get_signpost_json.cwl (CommandLineTool)
extract_ref_pac_signpost	../../tools/get_signpost_json.cwl (CommandLineTool)

Outputs

ID	Type	Label	Doc
token	File
harmonized_bam_uri	String