Skip to content
Permalink
Branch: master
Find file Copy path
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
39 lines (34 sloc) 803 Bytes
cwlVersion: v1.0
class: Workflow
id: bwa_mem_wf
requirements:
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement
inputs:
input_reads: File
indexed_reference_fasta: File
base_name: string
outputs:
aligned_bams:
type: File[]
outputSource: bwa_mem_split/output
steps:
bwa_input_prepare:
run: ../tools/bwa_input_prepare.cwl
in:
input_bam: input_reads
out: [output, rg]
expression_updatergsample:
run: ../tools/expression_preparerg.cwl
in:
rg: bwa_input_prepare/rg
sample: base_name
out: [rg_str]
bwa_mem_split:
run: ../tools/bwa_mem_split.cwl
in:
ref: indexed_reference_fasta
reads: bwa_input_prepare/output
rg: expression_updatergsample/rg_str
scatter: [reads]
out: [output]
You can’t perform that action at this time.