/
infuse_pipeline.cwl
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/
infuse_pipeline.cwl
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#!/usr/bin/env cwl-runner
class: Workflow
id: "infuseasdsada"
label: "workflow to detect fusion events"
cwlVersion: v1.0
requirements:
- class: InlineJavascriptRequirement
inputs:
in_bam:
type: File
doc: "input BAM file."
sample_name:
type: string
doc: "Sample name, which will used to prefix output file names."
tophat_fusion_reference:
type: File
doc: "Tophat fusion reference bundle tar file."
star_reference:
type: File
doc: "STAR reference bundle tar file."
defuse_reference:
type: File
doc: "Defuse reference bundle tar file."
gtf:
type: File
doc: "GTF file which is used to annotate break points."
vagrent_cache:
type: File
doc: "VAGrENT cache file that should be the same reference and gene build as the GTF file."
secondaryFiles:
- ".tbi"
- $(self.basename.replace("cache.gz", "fa"))
- $(self.basename.replace("cache.gz", "fa.fai"))
tophat_threads:
type: int?
default: 1
doc: "Number of threads to use for tophat fusion process."
star_threads:
type: int?
default: 1
doc: "Number of threads to use for tophat fusion process."
defuse_threads:
type: int?
default: 1
doc: "Number of threads to use for tophat fusion process."
outputs:
tophat_fusions:
type: File
outputSource: tophat_fusion/output
star_fusions:
type: File
outputSource: star_fusion/output
defuse_fusions:
type: File
outputSource: defuse/output
combined_fusions:
type: File
outputSource: combine_fusions/output
steps:
bam_to_fq:
in:
in_bam:
source: in_bam
out: [output_fqs]
run: tools/bam_to_fq.cwl
tophat_fusion:
in:
reads:
source: bam_to_fq/output_fqs
reference:
source: tophat_fusion_reference
sample_name:
source: sample_name
threads:
source: tophat_threads
out: [output]
run: tools/run-cgprna_tophat-fusion.cwl
star_fusion:
in:
reads:
source: bam_to_fq/output_fqs
reference:
source: star_reference
sample_name:
source: sample_name
threads:
source: star_threads
out: [output]
run: tools/run-cgprna_star-fusion.cwl
defuse:
in:
reads:
source: bam_to_fq/output_fqs
reference:
source: defuse_reference
sample_name:
source: sample_name
threads:
source: defuse_threads
out: [output]
run: tools/run-cgprna_defuse.cwl
combine_fusions:
in:
sample_name:
source: sample_name
gtf:
source: gtf
vagrent_cache:
source: vagrent_cache
tophat_fusion_output:
source: tophat_fusion/output
star_fusion_output:
source: star_fusion/output
defuse_output:
source: defuse/output
out: [output]
run: tools/compare_overlapping_fusions.cwl
doc: |
A workflow to run cpgRna Infuse pipeline from a single input BAM file (can be aligned or unaligned) of RNA-seq reads using cgpRna container. See the [cgpRna](https://github.com/cancerit/cgpRna) website for more information.
$schemas:
- http://schema.org/docs/schema_org_rdfa.html
$namespaces:
s: http://schema.org/
s:codeRepository: https://github.com/cancerit/cgpRna
s:license: https://spdx.org/licenses/AGPL-3.0
s:author:
- class: s:Person
s:email: mailto:yx2@sanger.ac.uk
s:name: Yaobo Xu