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tiling_convert2fastj_gvcf_named.cwl
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tiling_convert2fastj_gvcf_named.cwl
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$namespaces:
arv: "http://arvados.org/cwl#"
cwltool: "http://commonwl.org/cwltool#"
cwlVersion: v1.0
class: Workflow
label: Creates a FASTJ file per path for each named GVCF
requirements:
- class: DockerRequirement
dockerPull: arvados/l7g
- class: ResourceRequirement
coresMin: 2
coresMax: 2
- class: ScatterFeatureRequirement
hints:
arv:RuntimeConstraints:
keep_cache: 4096
cwltool:LoadListingRequirement:
loadListing: shallow_listing
inputs:
refdirectory:
type: Directory
label: Input Directory
datafilenames:
type: File
label: Files listing input gVCFs
ref:
type: string
label: Reference genome
reffa:
type: File
label: Reference genome in FASTA format
afn:
type: File
label: Compressed assembly fixed width file
aidx:
type: File
label: Assembly index file
refM:
type: string
label: Mitochondrial reference genome
reffaM:
type: File
label: Reference mitochondrial genome in FASTA format
afnM:
type: File
label: Compressed mitochondrial assembly fixed width file
aidxM:
type: File
label: Mitochondrial assembly index file
seqidM:
type: string
label: Mitochondrial naming scheme for gVCF
tagdir:
type: File
label: Compressed tagset in FASTA format
outputs:
out1:
type: Directory[]
outputSource: step2/out1
steps:
step1:
run: getdirs_testset.cwl
in:
datafilenames: datafilenames
refdirectory: refdirectory
out: [out1,out2]
step2:
scatter: [gffDir,gffPrefix]
scatterMethod: dotproduct
in:
gffDir: step1/out1
gffPrefix: step1/out2
ref: ref
reffa: reffa
afn: afn
aidx: aidx
refM: refM
reffaM: reffaM
afnM: afnM
aidxM: aidxM
seqidM: seqidM
tagdir: tagdir
run: convertgvcf.cwl
out: [out1,out2]