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class: Workflow
cwlVersion: v1.0
hints: []
inputs:
- id: alignment_rec
type:
fields:
- name: resources
type: string
- name: description
type: string
- name: config__algorithm__align_split_size
type:
- 'null'
- string
- name: files
type:
items: File
type: array
- name: config__algorithm__trim_reads
type:
- string
- 'null'
- boolean
- name: reference__fasta__base
type: File
- name: config__algorithm__adapters
type:
- 'null'
- string
- items:
- 'null'
- string
type: array
- name: rgnames__lb
type:
- 'null'
- string
- name: rgnames__rg
type: string
- name: rgnames__lane
type: string
- name: config__algorithm__bam_clean
type:
- string
- 'null'
- boolean
- name: config__algorithm__aligner
type: string
- name: reference__minimap2__indexes
type:
- 'null'
- string
- items:
- 'null'
- string
type: array
- name: rgnames__pl
type: string
- name: rgnames__pu
type: string
- name: config__algorithm__mark_duplicates
type:
- string
- 'null'
- boolean
- name: analysis
type: string
- name: rgnames__sample
type: string
name: alignment_rec
type: record
outputs:
- id: align_bam
outputSource: merge_split_alignments/align_bam
secondaryFiles:
- .bai
type:
- File
- 'null'
- id: work_bam_plus__disc
outputSource: merge_split_alignments/work_bam_plus__disc
secondaryFiles:
- .bai
type:
- File
- 'null'
- id: work_bam_plus__sr
outputSource: merge_split_alignments/work_bam_plus__sr
secondaryFiles:
- .bai
type:
- File
- 'null'
- id: hla__fastq
outputSource: merge_split_alignments/hla__fastq
type:
- 'null'
- items: File
type: array
requirements:
- class: EnvVarRequirement
envDef:
- envName: MPLCONFIGDIR
envValue: .
- class: ScatterFeatureRequirement
- class: SubworkflowFeatureRequirement
steps:
- id: prep_align_inputs
in:
- id: alignment_rec
source: alignment_rec
out:
- id: process_alignment_rec
run: steps/prep_align_inputs.cwl
- id: process_alignment
in:
- id: alignment_rec
source: alignment_rec
- id: process_alignment_rec
source: prep_align_inputs/process_alignment_rec
out:
- id: work_bam
- id: align_bam
- id: hla__fastq
- id: work_bam_plus__disc
- id: work_bam_plus__sr
run: steps/process_alignment.cwl
scatter:
- process_alignment_rec
scatterMethod: dotproduct
- id: merge_split_alignments
in:
- id: alignment_rec
source: alignment_rec
- id: work_bam
source: process_alignment/work_bam
- id: align_bam_toolinput
source: process_alignment/align_bam
- id: work_bam_plus__disc_toolinput
source: process_alignment/work_bam_plus__disc
- id: work_bam_plus__sr_toolinput
source: process_alignment/work_bam_plus__sr
- id: hla__fastq_toolinput
source: process_alignment/hla__fastq
out:
- id: align_bam
- id: work_bam_plus__disc
- id: work_bam_plus__sr
- id: hla__fastq
run: steps/merge_split_alignments.cwl
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