Workflow: regtools workflow

Fetched 2020-08-14 17:02:50 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

rna_tumor_bam File

RNAseq aligned tumor bam

e String[] (Optional)
transcriptome File

GTF file giving the transcriptome used to annotate against

i String[] (Optional)
variants File

VCF file providing somatic variant calls

Steps

ID Runs Label Doc
junctions_extract
junctions_extract.cwl (CommandLineTool)
cis_splice_effects
cis_splice_effects.cwl (CommandLineTool)
junctions_annotate
junctions_annotate.cwl (CommandLineTool)
cis_splice_effects_v2
cis_splice_effects_v2.cwl (CommandLineTool)
cis_splice_effects_v3
cis_splice_effects_v3.cwl (CommandLineTool)

Outputs

ID Type Label Doc
cis_splice_effects_identify_v2 File
cis_splice_effects_identify_v3 File
cis_splice_effects_identify File[]
junctions_extract_out File
junctions_annotate_out File
Permalink: https://w3id.org/cwl/view/git/c25ff825502cd51dbcf5aa72525ca9890cf8d70c/regtools/workflow.cwl