Workflow: etl.cwl

Fetched 2018-12-15 12:18:04 GMT
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Inputs

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

Steps

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

Outputs

ID Type Label Doc
harmonized_bam_uri String
token File
Permalink: https://w3id.org/cwl/view/git/b9b0dd5eb0b53bef93dafd896607c13dc74ea752/workflows/dnaseq/etl.cwl