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test.cwl
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test.cwl
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#!/usr/bin/env cwl-runner
label: "PGAP Pipeline"
cwlVersion: v1.0
class: Workflow
requirements:
- class: SubworkflowFeatureRequirement
- class: MultipleInputFeatureRequirement
# - class: DockerRequirement
# dockerPull: ncbi/gpdev:latest
inputs:
hmm_hits: File
hmm_search_proteins: File
outfull: File
univ_prot_xml: File
val_res_den_xml: File
steps:
test:
run: ../..//bact_univ_prot_stats.cwl
in:
annot_request_id:
default: -1 # this is dummy annot_request_id
hmm_search: hmm_hits # bacterial_annot_3_Search_Naming_HMMs_hmm_hits_bypass # for bacterial_annot_3/Search_Naming_HMMs_hmm_hits # Search Naming HMMs bacterial_annot 3
hmm_search_proteins: hmm_search_proteins # bacterial_annot_3_Run_GeneMark_Post_models_bypass # for bacterial_annot_3/Run_GeneMark_Post_models # genemark models
input: outfull # Final_Bacterial_Package_final_bact_asn/outfull
univ_prot_xml: univ_prot_xml # /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/home/badrazat/local-install/2018-05-17/third-party/data/BacterialPipeline/uniColl/ver-3.2/universal.xml
val_res_den_xml: val_res_den_xml # /panfs/pan1.be-md.ncbi.nlm.nih.gov/gpipe/home/badrazat/local-install/2018-05-17/etc/validation-results.xml
it:
default: true
out: [bact_univ_prot_stats_old_xml, var_bact_univ_prot_details_xml, var_bact_univ_prot_stats_xml]
outputs:
bact_univ_prot_stats_old_xml:
type: File
outputSource: test/bact_univ_prot_stats_old_xml
var_bact_univ_prot_details_xml:
type: File
outputSource: test/var_bact_univ_prot_details_xml
var_bact_univ_prot_stats_xml:
type: File
outputSource: test/var_bact_univ_prot_stats_xml