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#!/usr/bin/env cwl-runner
cwlVersion: v1.0
class: Workflow
label: "regtools workflow"
requirements:
- class: ScatterFeatureRequirement
inputs:
rna_tumor_bam:
type: File
doc: RNAseq aligned tumor bam
reference:
type: File
doc: Fasta file containing the reference corresponding to the bam files
transcriptome:
type: File
doc: GTF file giving the transcriptome used to annotate against
variants:
type: File
doc: VCF file providing somatic variant calls
e:
type: string[]?
default: ["2", "5"]
i:
type: string[]?
default: ["3", "50"]
outputs:
cis_splice_effects_identify:
type: File[]
outputSource: cis_splice_effects/aberrant_splice_junctions
cis_splice_effects_identify_v2:
type: File
outputSource: cis_splice_effects_v2/aberrant_splice_junctions
cis_splice_effects_identify_v3:
type: File
outputSource: cis_splice_effects_v3/aberrant_splice_junctions
junctions_extract_out:
type: File
outputSource: junctions_extract/junctions
junctions_annotate_out:
type: File
outputSource: junctions_annotate/junctions_annotated
steps:
cis_splice_effects:
scatter: [ e, i ]
scatterMethod: dotproduct
run: cis_splice_effects.cwl
in:
e: e
i: i
variants: variants
bam: rna_tumor_bam
ref: reference
gtf: transcriptome
out: [ aberrant_splice_junctions ]
cis_splice_effects_v2:
run: cis_splice_effects_v2.cwl
in:
variants: variants
bam: rna_tumor_bam
ref: reference
gtf: transcriptome
out: [ aberrant_splice_junctions ]
cis_splice_effects_v3:
run: cis_splice_effects_v3.cwl
in:
variants: variants
bam: rna_tumor_bam
ref: reference
gtf: transcriptome
out: [ aberrant_splice_junctions ]
junctions_extract:
run: junctions_extract.cwl
in:
bam: rna_tumor_bam
out: [ junctions ]
junctions_annotate:
run: junctions_annotate.cwl
in:
junctions: junctions_extract/junctions
ref: reference
gtf: transcriptome
out: [ junctions_annotated ]
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