Workflow: gdc workflow

Fetched 2021-03-03 21:02:43 GMT
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Workflow as SVG
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  • Inputs/Outputs

Inputs

ID Type Title Doc
reference File

Fasta file containing the reference corresponding to the bam files

transcriptome File

GTF file giving the transcriptome used to annotate against

tcga_sample String

String giving the TCGA sample id, i.e. TCGA-01-0001-01A

gdc_token File

gdc_token providing permission for downloading controlled access data

Steps

ID Runs Label Doc
filter_vcf
filter_vcf.cwl (CommandLineTool)
bgzip_vcf
bgzip_vcf.cwl (CommandLineTool)
download_vcf
download_vcf.cwl (CommandLineTool)
regtools regtools workflow
obtain_manifest_vcf
obtain_manifest_vcf.cwl (CommandLineTool)
download_bam
download_bam.cwl (CommandLineTool)
merge_vcf
merge_vcf.cwl (CommandLineTool)
decompress_vcf
decompress_vcf.cwl (CommandLineTool)
obtain_manifest_bam
obtain_manifest_bam.cwl (CommandLineTool)
index_vcf
index_vcf.cwl (CommandLineTool)

Outputs

ID Type Label Doc
filtered_vcf_file File
Permalink: https://w3id.org/cwl/view/git/c25ff825502cd51dbcf5aa72525ca9890cf8d70c/gdc_client/workflow.cwl