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main.cwl
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cwlVersion: v1.2
class: Workflow
$namespaces:
s: https://schema.org/
$schemas:
- https://schema.org/version/latest/schemaorg-current-http.rdf
s:author:
- class: s:Person
s:identifier: https://orcid.org/0000-0001-9290-2017
s:email: mailto:[email protected]
s:name: Iacopo Colonnelli
s:codeRepository: https://github.com/alpha-unito/cwl-1000genome-workflow
s:dateCreated: "2022-09-28"
s:license: https://spdx.org/licenses/Apache-2.0
requirements:
ScatterFeatureRequirement: {}
SubworkflowFeatureRequirement: {}
inputs:
columns_file: File
frequency_script: File
individuals_script: File
individuals_merge_script: File
mutation_overlap_script: File
populations: File[]
sift_files: File[]
sifting_script: File
snp_files: File[]
step: int
total: int
outputs:
overlap_files:
type:
type: array
items:
type: array
items: File
outputSource: chromosome/overlap_files
freq_files:
type:
type: array
items:
type: array
items: File
outputSource: chromosome/freq_files
steps:
chromosome:
in:
columns_file: columns_file
frequency_script: frequency_script
individuals_script: individuals_script
individuals_merge_script: individuals_merge_script
mutation_overlap_script: mutation_overlap_script
step: step
populations: populations
sift_file: sift_files
sifting_script: sifting_script
snp_file: snp_files
total: total
scatter:
- sift_file
- snp_file
scatterMethod: dotproduct
out: [overlap_files, freq_files]
run:
class: Workflow
inputs:
columns_file: File
frequency_script: File
individuals_script: File
individuals_merge_script: File
mutation_overlap_script: File
step: int
populations: File[]
sift_file: File
sifting_script: File
snp_file: File
total: int
outputs:
overlap_files:
type: File[]
outputSource: mutation_overlap/output_file
freq_files:
type: File[]
outputSource: frequency/output_file
steps:
get_chromosome:
in:
snp_file: snp_file
out: [chromosome]
run: clt/get_chromosome.cwl
get_intervals:
in:
step: step
total: total
out: [counters, stops]
run: clt/get_intervals.cwl
individuals:
in:
script: individuals_script
input_file: snp_file
columns_file: columns_file
chromosome: get_chromosome/chromosome
counter: get_intervals/counters
stop: get_intervals/stops
total: total
scatter:
- counter
- stop
scatterMethod: dotproduct
out: [output_file]
run: clt/individuals.cwl
individuals_merge:
in:
script: individuals_merge_script
chromosome: get_chromosome/chromosome
individuals: individuals/output_file
out: [output_file]
run: clt/individuals_merge.cwl
sifting:
in:
script: sifting_script
input_file: sift_file
chromosome: get_chromosome/chromosome
out: [output_file]
run: clt/sifting.cwl
mutation_overlap:
in:
script: mutation_overlap_script
input_file: individuals_merge/output_file
chromosome: get_chromosome/chromosome
population: populations
sift_file: sifting/output_file
columns_file: columns_file
scatter: population
out: [output_file]
run: clt/mutation_overlap.cwl
frequency:
in:
script: frequency_script
input_file: individuals_merge/output_file
chromosome: get_chromosome/chromosome
population: populations
sift_file: sifting/output_file
columns_file: columns_file
scatter: population
out: [output_file]
run: clt/frequency.cwl