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ici-workflow.cwl
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ici-workflow.cwl
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cwlVersion: v1.2
class: Workflow
label: ici-workflows
$namespaces:
sbg: https://sevenbridges.com
requirements:
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
- class: InlineJavascriptRequirement
- class: StepInputExpressionRequirement
inputs:
- id: vcf_file
label: Variants Files
doc: Input Variants Files.
type: File[]?
sbg:fileTypes: VCF, VCF.GZ, BCF, BCF.GZ
sbg:x: -399
sbg:y: -230
- id: phenotype_data
type: File
sbg:x: -189.47531127929688
sbg:y: -316.4203186035156
- id: custom_input
label: RUN VCF 2 GDS
type: boolean
sbg:x: -405.90972900390625
sbg:y: 20.418041229248047
- id: gds
type: File
sbg:x: -157.79391479492188
sbg:y: 195.00299072265625
outputs:
- id: csv_output
type: File?
outputSource:
- instance_specific_causal/csv_output
sbg:x: 527.6246948242188
sbg:y: -22.258909225463867
- id: dict
type: File?
outputSource:
- instance_specific_causal/dict
sbg:x: 490.1069030761719
sbg:y: -299.4132995605469
steps:
- id: instance_specific_causal
label: instance-specific-causal
in:
- id: genomic_data
source: unzip/unzipped_file
pickValue: the_only_non_null
- id: phenotype_data
source: phenotype_data
- id: output_file_prefix
default: test
run: ici-workflow.cwl.steps/instance_specific_causal.cwl
out:
- id: csv_output
- id: dict
sbg:x: 252.208740234375
sbg:y: -211.32017517089844
- id: vcf_to_gds
label: VCF to GDS converter
in:
- id: vcf_file
source:
- vcf_file
- id: check_gds_1
default: No
- id: custom_input
source: custom_input
run: ici-workflow.cwl.steps/vcf_to_gds.cwl
when: $(inputs.custom_input)
out:
- id: unique_variant_id_gds_per_chr
sbg:x: -221
sbg:y: -131
- id: seq_array_preprocess
label: seq-array-preprocess
in:
- id: phenotypes
source: phenotype_data
- id: gds
source:
- vcf_to_gds/unique_variant_id_gds_per_chr
- gds
pickValue: the_only_non_null
run: ici-workflow.cwl.steps/seq_array_preprocess.cwl
out:
- id: processed_vcf
sbg:x: -38.37094497680664
sbg:y: -141.0281982421875
- id: unzip
label: gunzip
in:
- id: input_file
source: seq_array_preprocess/processed_vcf
run: ici-workflow.cwl.steps/unzip.cwl
out:
- id: unzipped_file
sbg:x: 115.94216918945312
sbg:y: -122.71649932861328
sbg:appVersion:
- v1.2
- v1.1
sbg:content_hash: acacb964451ee2d83db405955abca0c8a287e833963e2a0139af1b6fc50d9afde
sbg:contributors:
- dave
sbg:createdBy: dave
sbg:createdOn: 1620320385
sbg:id: dave/build-instance-specific-casual-inference/ici-workflows/17
sbg:image_url: |-
https://platform.sb.biodatacatalyst.nhlbi.nih.gov/ns/brood/images/dave/build-instance-specific-casual-inference/ici-workflows/17.png
sbg:latestRevision: 17
sbg:modifiedBy: dave
sbg:modifiedOn: 1626725658
sbg:original_source: |-
https://api.sb.biodatacatalyst.nhlbi.nih.gov/v2/apps/dave/build-instance-specific-casual-inference/ici-workflows/17/raw/
sbg:project: dave/build-instance-specific-casual-inference
sbg:projectName: 'BUILD: Instance Specific Casual Inference'
sbg:publisher: sbg
sbg:revision: 17
sbg:revisionNotes: ''
sbg:revisionsInfo:
- sbg:modifiedBy: dave
sbg:modifiedOn: 1620320385
sbg:revision: 0
sbg:revisionNotes:
- sbg:modifiedBy: dave
sbg:modifiedOn: 1620320532
sbg:revision: 1
sbg:revisionNotes: ''
- sbg:modifiedBy: dave
sbg:modifiedOn: 1621972158
sbg:revision: 2
sbg:revisionNotes: ''
- sbg:modifiedBy: dave
sbg:modifiedOn: 1621972244
sbg:revision: 3
sbg:revisionNotes: added conditional
- sbg:modifiedBy: dave
sbg:modifiedOn: 1621972294
sbg:revision: 4
sbg:revisionNotes: ''
- sbg:modifiedBy: dave
sbg:modifiedOn: 1621972638
sbg:revision: 5
sbg:revisionNotes: single element
- sbg:modifiedBy: dave
sbg:modifiedOn: 1621972691
sbg:revision: 6
sbg:revisionNotes: no scatter
- sbg:modifiedBy: dave
sbg:modifiedOn: 1621973366
sbg:revision: 7
sbg:revisionNotes: ''
- sbg:modifiedBy: dave
sbg:modifiedOn: 1621973413
sbg:revision: 8
sbg:revisionNotes: added preprocess.r
- sbg:modifiedBy: dave
sbg:modifiedOn: 1621973515
sbg:revision: 9
sbg:revisionNotes: ''
- sbg:modifiedBy: dave
sbg:modifiedOn: 1621974202
sbg:revision: 10
sbg:revisionNotes: ''
- sbg:modifiedBy: dave
sbg:modifiedOn: 1621975273
sbg:revision: 11
sbg:revisionNotes: ''
- sbg:modifiedBy: dave
sbg:modifiedOn: 1625850605
sbg:revision: 12
sbg:revisionNotes: '"remove minor = T"'
- sbg:modifiedBy: dave
sbg:modifiedOn: 1625851572
sbg:revision: 13
sbg:revisionNotes: ''
- sbg:modifiedBy: dave
sbg:modifiedOn: 1625852253
sbg:revision: 14
sbg:revisionNotes: ''
- sbg:modifiedBy: dave
sbg:modifiedOn: 1625853557
sbg:revision: 15
sbg:revisionNotes: ''
- sbg:modifiedBy: dave
sbg:modifiedOn: 1626725555
sbg:revision: 16
sbg:revisionNotes: ''
- sbg:modifiedBy: dave
sbg:modifiedOn: 1626725658
sbg:revision: 17
sbg:revisionNotes: ''
sbg:sbgMaintained: false
sbg:validationErrors: []