@prefix NetworkAccess: .
@prefix rdf: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix cwl: .
@prefix Workflow: .
@prefix ResourceRequirement: .
@prefix sld: .
@prefix CommandOutputBinding: .
@prefix ns1: .
cwl:source .
a cwl:CommandLineTool ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 4 ;
ResourceRequirement:outdirMin 358400 ;
ResourceRequirement:ramMin 1.525879e+04
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "dnastack/plink:1.9"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 4 ;
ResourceRequirement:outdirMin 358400 ;
ResourceRequirement:ramMin 1.525879e+04
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "dnastack/plink:1.9"
] ;
cwl:inputs , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nplink \\\n\t--vcf $(inputs.vcf.path) \\\n\t--maf 0.10 \\\n\t--update-ids $(inputs.ids.path) \\\n\t--make-bed \\\n\t--out $(inputs.vcf.path.replace(\"\\\\?.*\", \"\") .split('/').reverse()[0].replace(/\\.vcf\\.gz$/, ''))\n\nplink \\\n\t--bfile $(inputs.vcf.path.replace(\"\\\\?.*\", \"\") .split('/').reverse()[0].replace(/\\.vcf\\.gz$/, '')) \\\n\t--update-sex $(inputs.sex.path) \\\n\t--pheno $(inputs.phenotypes.path) \\\n\t--make-bed \\\n\t--out $(inputs.vcf.path.replace(\"\\\\?.*\", \"\") .split('/').reverse()[0].replace(/\\.vcf\\.gz$/, ''))\n\n# Recode covariates to binary\nplink \\\n\t--bfile $(inputs.vcf.path.replace(\"\\\\?.*\", \"\") .split('/').reverse()[0].replace(/\\.vcf\\.gz$/, '')) \\\n\t--covar $(inputs.covariates.path) \\\n\t--dummy-coding \\\n\t--write-covar\n\nplink \\\n\t--bfile $(inputs.vcf.path.replace(\"\\\\?.*\", \"\") .split('/').reverse()[0].replace(/\\.vcf\\.gz$/, '')) \\\n\t--logistic \\\n\t--covar plink.cov \\\n\t--out $(inputs.vcf.path.replace(\"\\\\?.*\", \"\") .split('/').reverse()[0].replace(/\\.vcf\\.gz$/, ''))\n\nsed -i -e 's/\\s\\+/,/g' -e 's/^,//g' -e 's/,$//g' $(inputs.vcf.path.replace(\"\\\\?.*\", \"\") .split('/').reverse()[0].replace(/\\.vcf\\.gz$/, '')).assoc.logistic\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nplink \\\n\t--vcf $(inputs.vcf.path) \\\n\t--maf 0.10 \\\n\t--update-ids $(inputs.ids.path) \\\n\t--make-bed \\\n\t--out $(inputs.vcf.path.replace(\"\\\\?.*\", \"\") .split('/').reverse()[0].replace(/\\.vcf\\.gz$/, ''))\n\nplink \\\n\t--bfile $(inputs.vcf.path.replace(\"\\\\?.*\", \"\") .split('/').reverse()[0].replace(/\\.vcf\\.gz$/, '')) \\\n\t--update-sex $(inputs.sex.path) \\\n\t--pheno $(inputs.phenotypes.path) \\\n\t--make-bed \\\n\t--out $(inputs.vcf.path.replace(\"\\\\?.*\", \"\") .split('/').reverse()[0].replace(/\\.vcf\\.gz$/, ''))\n\n# Recode covariates to binary\nplink \\\n\t--bfile $(inputs.vcf.path.replace(\"\\\\?.*\", \"\") .split('/').reverse()[0].replace(/\\.vcf\\.gz$/, '')) \\\n\t--covar $(inputs.covariates.path) \\\n\t--dummy-coding \\\n\t--write-covar\n\nplink \\\n\t--bfile $(inputs.vcf.path.replace(\"\\\\?.*\", \"\") .split('/').reverse()[0].replace(/\\.vcf\\.gz$/, '')) \\\n\t--logistic \\\n\t--covar plink.cov \\\n\t--out $(inputs.vcf.path.replace(\"\\\\?.*\", \"\") .split('/').reverse()[0].replace(/\\.vcf\\.gz$/, ''))\n\nsed -i -e 's/\\s\\+/,/g' -e 's/^,//g' -e 's/,$//g' $(inputs.vcf.path.replace(\"\\\\?.*\", \"\") .split('/').reverse()[0].replace(/\\.vcf\\.gz$/, '')).assoc.logistic\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] .
cwl:outputSource ;
sld:type cwl:File .
sld:type cwl:File .
cwl:source .
sld:type cwl:File .
sld:type cwl:File .
sld:type cwl:File .
cwl:in , ;
cwl:out ;
cwl:run .
sld:type cwl:File .
cwl:source .
a cwl:Workflow ;
ns1:original_cwlVersion "v1.2" ;
Workflow:steps , , ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.assoc_file.basename.replace(/\\.assoc\\.logistic$/, '') + \".png\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.assoc_file.basename.replace(/\\.assoc\\.logistic$/, '') + \".png\")" ] ;
sld:type cwl:File .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"phenotypes.txt" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"phenotypes.txt" ] ;
sld:type cwl:File .
sld:type xsd:int .
cwl:outputBinding [ CommandOutputBinding:glob
"ids.txt" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"ids.txt" ] ;
sld:type cwl:File .
sld:type cwl:File .
sld:type xsd:int .
sld:type cwl:File .
cwl:source .
cwl:in ;
cwl:out , , , ;
cwl:run .
a cwl:CommandLineTool ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "dnastack/plink:1.9"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 2 ;
ResourceRequirement:outdirMin 20480 ;
ResourceRequirement:ramMin 7.152557e+03
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "dnastack/plink:1.9"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 2 ;
ResourceRequirement:outdirMin 20480 ;
ResourceRequirement:ramMin 7.152557e+03
] ;
cwl:inputs , ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nmanhattan_plot.py \\\n\t-i $(inputs.assoc_file.path) \\\n\t-c $(inputs.chromnum) \\\n\t-o $(inputs.assoc_file.basename.replace(/\\.assoc\\.logistic$/, '') ).png\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nmanhattan_plot.py \\\n\t-i $(inputs.assoc_file.path) \\\n\t-c $(inputs.chromnum) \\\n\t-o $(inputs.assoc_file.basename.replace(/\\.assoc\\.logistic$/, '') ).png\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:source .
a cwl:CommandLineTool ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "dnastack/plink:1.9"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin 20480 ;
ResourceRequirement:ramMin 3.576279e+03
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin 20480 ;
ResourceRequirement:ramMin 3.576279e+03
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "dnastack/plink:1.9"
] ;
cwl:inputs ;
cwl:outputs , , , ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nparse_metadata.sh \\\n\t-c $(inputs.metadata_csv.path)\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nparse_metadata.sh \\\n\t-c $(inputs.metadata_csv.path)\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] .
cwl:outputSource ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"covariates.txt" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"covariates.txt" ] ;
sld:type cwl:File .
sld:type cwl:File .
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"sex.txt" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"sex.txt" ] ;
sld:type cwl:File .
cwl:source .
cwl:in , , , , ;
cwl:out ;
cwl:run .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.vcf.path.replace(\"\\\\?.*\", \"\") .split('/').reverse()[0].replace(/\\.vcf\\.gz$/, '') + \".assoc.logistic\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.vcf.path.replace(\"\\\\?.*\", \"\") .split('/').reverse()[0].replace(/\\.vcf\\.gz$/, '') + \".assoc.logistic\")" ] ;
sld:type cwl:File .
cwl:source .