forked from kids-first/kf-alignment-workflow
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kfdrc_process_se_set.cwl
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kfdrc_process_se_set.cwl
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cwlVersion: v1.0
class: Workflow
id: kfdrc_process_se_set
requirements:
- class: ScatterFeatureRequirement
- class: MultipleInputFeatureRequirement
- class: SubworkflowFeatureRequirement
inputs:
input_se_reads: File
input_se_rgs: string
indexed_reference_fasta:
type: File
secondaryFiles: ['.64.amb', '.64.ann', '.64.bwt', '.64.pac', '.64.sa', '.64.alt', '^.dict']
min_alignment_score: int?
outputs:
unsorted_bams:
type: File[]
outputSource: bwa_mem_split_se_reads/output
steps:
zcat_split_reads:
hints:
- class: 'sbg:AWSInstanceType'
value: c5.9xlarge
run: ../tools/fastq_chomp.cwl
in:
input_fastq: input_se_reads
out: [output]
bwa_mem_split_se_reads:
run: ../tools/bwa_mem_naive.cwl
in:
ref: indexed_reference_fasta
reads: zcat_split_reads/output
rg: input_se_rgs
min_alignment_score: min_alignment_score
scatter: reads
out: [output] #+0 Nesting File[]
$namespaces:
sbg: https://sevenbridges.com
hints:
- class: 'sbg:maxNumberOfParallelInstances'
value: 4