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class: Workflow
cwlVersion: v1.0
hints: []
inputs:
- id: batch_rec
type:
items:
fields:
- name: resources
type: string
- name: description
type: string
- name: reference__fasta__base
type: File
- name: config__algorithm__variantcaller
type: string
- name: reference__snpeff__GRCh37_75
type: File
- name: config__algorithm__coverage_interval
type:
- string
- 'null'
- name: genome_resources__variation__train_hapmap
type: File
- name: genome_resources__variation__encode_blacklist
type: File
- name: metadata__batch
type:
- 'null'
- string
- name: genome_resources__variation__lcr
type: File
- name: vrn_file
type:
- 'null'
- string
- name: reference__twobit
type: File
- name: config__algorithm__validate
type: File
- name: config__algorithm__validate_regions
type: File
- name: genome_build
type: string
- name: metadata__phenotype
type: string
- name: genome_resources__aliases__human
type:
- string
- 'null'
- boolean
- name: config__algorithm__tools_off
type:
items: string
type: array
- name: genome_resources__variation__dbsnp
type: File
- name: genome_resources__variation__polyx
type: File
- name: genome_resources__variation__cosmic
type: File
- name: reference__genome_context
type:
items: File
type: array
- name: analysis
type: string
- name: config__algorithm__tools_on
type:
- 'null'
- string
- items:
- 'null'
- string
type: array
- name: config__algorithm__effects
type:
- string
- 'null'
- boolean
- name: config__algorithm__variant_regions
type:
- File
- 'null'
- name: genome_resources__aliases__ensembl
type: string
- name: config__algorithm__exclude_regions
type:
- 'null'
- string
- items:
- 'null'
- string
type: array
- name: reference__rtg
type: File
- name: genome_resources__variation__train_indels
type: File
- name: genome_resources__aliases__snpeff
type: string
- name: align_bam
type:
- File
- 'null'
- name: regions__sample_callable
type:
- File
- 'null'
- name: config__algorithm__callable_regions
type: File
name: batch_rec
type: record
type: array
outputs:
- id: vc_rec
outputSource: compare_to_rm/vc_rec
type:
items:
fields:
- name: batch_samples
type:
- 'null'
- items: string
type: array
- name: validate__summary
type:
- File
- 'null'
- name: validate__tp
type:
- File
- 'null'
- name: validate__fp
type:
- File
- 'null'
- name: validate__fn
type:
- File
- 'null'
- name: resources
type: string
- name: description
type: string
- name: vrn_file
type: File
- name: reference__fasta__base
type: File
- name: config__algorithm__variantcaller
type: string
- name: config__algorithm__coverage_interval
type:
- string
- 'null'
- name: metadata__batch
type:
- 'null'
- string
- name: config__algorithm__validate
type: File
- name: config__algorithm__validate_regions
type: File
- name: genome_build
type: string
- name: metadata__phenotype
type: string
- name: genome_resources__aliases__human
type:
- string
- 'null'
- boolean
- name: config__algorithm__tools_off
type:
items: string
type: array
- name: reference__genome_context
type:
items: File
type: array
- name: analysis
type: string
- name: config__algorithm__tools_on
type:
- 'null'
- string
- items:
- 'null'
- string
type: array
- name: config__algorithm__effects
type:
- string
- 'null'
- boolean
- name: config__algorithm__variant_regions
type:
- File
- 'null'
- name: genome_resources__aliases__ensembl
type: string
- name: config__algorithm__exclude_regions
type:
- 'null'
- string
- items:
- 'null'
- string
type: array
- name: genome_resources__aliases__snpeff
type: string
- name: regions__sample_callable
type:
- File
- 'null'
- name: config__algorithm__callable_regions
type: File
name: vc_rec
type: record
type: array
requirements:
- class: EnvVarRequirement
envDef:
- envName: MPLCONFIGDIR
envValue: .
- class: ScatterFeatureRequirement
- class: SubworkflowFeatureRequirement
steps:
- id: get_parallel_regions
in:
- id: batch_rec
source: batch_rec
out:
- id: region_block
run: steps/get_parallel_regions.cwl
- id: variantcall_batch_region
in:
- id: batch_rec
source: batch_rec
- id: region_block_toolinput
source: get_parallel_regions/region_block
out:
- id: vrn_file_region
- id: region_block
run: steps/variantcall_batch_region.cwl
scatter:
- region_block_toolinput
scatterMethod: dotproduct
- id: concat_batch_variantcalls
in:
- id: batch_rec
source: batch_rec
- id: region_block
source: variantcall_batch_region/region_block
- id: vrn_file_region
source: variantcall_batch_region/vrn_file_region
out:
- id: vrn_file
run: steps/concat_batch_variantcalls.cwl
- id: postprocess_variants
in:
- id: batch_rec
source: batch_rec
- id: vrn_file_toolinput
source: concat_batch_variantcalls/vrn_file
out:
- id: vrn_file
run: steps/postprocess_variants.cwl
- id: compare_to_rm
in:
- id: batch_rec
source: batch_rec
- id: vrn_file
source: postprocess_variants/vrn_file
out:
- id: vc_rec
run: steps/compare_to_rm.cwl
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