@prefix NetworkAccess: .
@prefix rdf: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix cwl: .
@prefix Workflow: .
@prefix ResourceRequirement: .
@prefix sld: .
@prefix CommandOutputBinding: .
@prefix ns1: .
cwl:outputBinding [ CommandOutputBinding:glob
"monitoring.log" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"monitoring.log" ] ;
sld:type cwl:File .
sld:type cwl:File , sld:null .
cwl:in , ;
cwl:out , ;
cwl:run .
sld:type cwl:File , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"monitoring.log" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"monitoring.log" ] ;
sld:type cwl:File .
cwl:source .
sld:default "BS_CT" .
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 "quay.io/biocontainers/picard:2.18.3--py27_0"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/picard:2.18.3--py27_0"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin "$((Math.ceil(2 * (function(size_of=0){inputs.reference_fasta.forEach(function(element){ if (element) {size_of += element.size}})}) / 1000^3 < 1 ? 1 : (function(size_of=0){inputs.reference_fasta.forEach(function(element){ if (element) {size_of += element.size}})}) / 1000^3) ) * 1024)" ;
ResourceRequirement:ramMin 4e+03
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin "$((Math.ceil(2 * (function(size_of=0){inputs.reference_fasta.forEach(function(element){ if (element) {size_of += element.size}})}) / 1000^3 < 1 ? 1 : (function(size_of=0){inputs.reference_fasta.forEach(function(element){ if (element) {size_of += element.size}})}) / 1000^3) ) * 1024)" ;
ResourceRequirement:ramMin 4e+03
] ;
cwl:inputs , ;
cwl:outputs , ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nset -euo pipefail\n\n# if the WDL/task contains a monitoring script as input\nif [ ! -z \"$(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path)\" ]; then\n chmod a+x $(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path)\n $(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path) > monitoring.log &\nelse\n echo \"No monitoring script given as input\" > monitoring.log &\nfi\n\n# create a reference dict\njava -Xmx3500m -jar /usr/local/share/picard-2.18.3-0/picard.jar CreateSequenceDictionary \\\n REFERENCE=$(inputs.reference_fasta.path) \\\n OUTPUT=$(inputs.reference_fasta.basename.replace(/\\.fa$/, '') .split('/').reverse()[0].replace(/\\.fasta$/, '') + \".dict\")\nsed -i \"s=\\$(dirname $(inputs.reference_fasta.path))/==g\" $(inputs.reference_fasta.basename.replace(/\\.fa$/, '') .split('/').reverse()[0].replace(/\\.fasta$/, '') + \".dict\") # for reproducibility\n\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nset -euo pipefail\n\n# if the WDL/task contains a monitoring script as input\nif [ ! -z \"$(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path)\" ]; then\n chmod a+x $(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path)\n $(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path) > monitoring.log &\nelse\n echo \"No monitoring script given as input\" > monitoring.log &\nfi\n\n# create a reference dict\njava -Xmx3500m -jar /usr/local/share/picard-2.18.3-0/picard.jar CreateSequenceDictionary \\\n REFERENCE=$(inputs.reference_fasta.path) \\\n OUTPUT=$(inputs.reference_fasta.basename.replace(/\\.fa$/, '') .split('/').reverse()[0].replace(/\\.fasta$/, '') + \".dict\")\nsed -i \"s=\\$(dirname $(inputs.reference_fasta.path))/==g\" $(inputs.reference_fasta.basename.replace(/\\.fa$/, '') .split('/').reverse()[0].replace(/\\.fasta$/, '') + \".dict\") # for reproducibility\n\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
sld:type xsd:string .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.reference_fasta.basename + \".fai\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.reference_fasta.basename + \".fai\")" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(\"genome_mfa.CT_conversion.fa\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(\"genome_mfa.CT_conversion.fa\")" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/mr_c/bisulfite-references:1.0"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin "$((Math.ceil(3.5 * (function(size_of=0){inputs.fasta_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1000^3 < 1 ? 1 : (function(size_of=0){inputs.fasta_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1000^3) ) * 1024)" ;
ResourceRequirement:ramMin 3.33786e+03
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin "$((Math.ceil(3.5 * (function(size_of=0){inputs.fasta_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1000^3 < 1 ? 1 : (function(size_of=0){inputs.fasta_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1000^3) ) * 1024)" ;
ResourceRequirement:ramMin 3.33786e+03
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/mr_c/bisulfite-references:1.0"
] ;
cwl:inputs , ;
cwl:outputs , , ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\n# if the WDL/task contains a monitoring script as input\nif [ ! -z \"$(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path)\" ]; then\n chmod a+x $(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path)\n $(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path) > monitoring.log &\nelse\n echo \"No monitoring script given as input\" > monitoring.log &\nfi\n\npython3 /build_bisulfite_references.py \\\n --input-fasta $(inputs.fasta_input.path) \\\n --forward-convert-out $(\"genome_mfa.CT_conversion.fa\") \\\n --reverse-convert-out $(\"genome_mfa.GA_conversion.fa\")\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\n# if the WDL/task contains a monitoring script as input\nif [ ! -z \"$(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path)\" ]; then\n chmod a+x $(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path)\n $(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path) > monitoring.log &\nelse\n echo \"No monitoring script given as input\" > monitoring.log &\nfi\n\npython3 /build_bisulfite_references.py \\\n --input-fasta $(inputs.fasta_input.path) \\\n --forward-convert-out $(\"genome_mfa.CT_conversion.fa\") \\\n --reverse-convert-out $(\"genome_mfa.GA_conversion.fa\")\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:source .
sld:type xsd:string .
cwl:in , , ;
cwl:out , ;
cwl:run .
sld:type cwl:File .
sld:type cwl:File .
cwl:source .
cwl:outputSource ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:outputBinding [ CommandOutputBinding:glob
"monitoring.log" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"monitoring.log" ] ;
sld:type cwl:File .
cwl:source .
a cwl:CommandLineTool ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin "$((Math.ceil(2.25 * (function(size_of=0){inputs.reference_fasta.forEach(function(element){ if (element) {size_of += element.size}})}) / 1000^3 < 1 ? 1 : (function(size_of=0){inputs.reference_fasta.forEach(function(element){ if (element) {size_of += element.size}})}) / 1000^3) ) * 1024)" ;
ResourceRequirement:ramMin 3.33786e+03
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.9--h10a08f8_12"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin "$((Math.ceil(2.25 * (function(size_of=0){inputs.reference_fasta.forEach(function(element){ if (element) {size_of += element.size}})}) / 1000^3 < 1 ? 1 : (function(size_of=0){inputs.reference_fasta.forEach(function(element){ if (element) {size_of += element.size}})}) / 1000^3) ) * 1024)" ;
ResourceRequirement:ramMin 3.33786e+03
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.9--h10a08f8_12"
] ;
cwl:inputs , ;
cwl:outputs , ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nset -euo pipefail\n\n# if the WDL/task contains a monitoring script as input\nif [ ! -z \"$(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path)\" ]; then\n chmod a+x $(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path)\n $(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path) > monitoring.log &\nelse\n echo \"No monitoring script given as input\" > monitoring.log &\nfi\n\ndeclare -a FASTA_TEMP=\\$(mktemp fasta_XXXXXX)\ncp $(inputs.reference_fasta.path) $FASTA_TEMP\n\n# create a reference index\nsamtools faidx \\\n $FASTA_TEMP\n\nmv $FASTA_TEMP.fai $(inputs.reference_fasta.basename + \".fai\")\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nset -euo pipefail\n\n# if the WDL/task contains a monitoring script as input\nif [ ! -z \"$(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path)\" ]; then\n chmod a+x $(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path)\n $(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path) > monitoring.log &\nelse\n echo \"No monitoring script given as input\" > monitoring.log &\nfi\n\ndeclare -a FASTA_TEMP=\\$(mktemp fasta_XXXXXX)\ncp $(inputs.reference_fasta.path) $FASTA_TEMP\n\n# create a reference index\nsamtools faidx \\\n $FASTA_TEMP\n\nmv $FASTA_TEMP.fai $(inputs.reference_fasta.basename + \".fai\")\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:source .
cwl:in , , ;
cwl:out , ;
cwl:run .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:in , ;
cwl:out , , ;
cwl:run .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.index_prefix + \"*\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.index_prefix + \"*\")" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
cwl:in , ;
cwl:out , ;
cwl:run .
a cwl:CommandLineTool ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin "$((Math.ceil(3 * (function(size_of=0){inputs.fasta_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1000^3 < 1 ? 1 : (function(size_of=0){inputs.fasta_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1000^3) ) * 1024)" ;
ResourceRequirement:ramMin 6.67572e+03
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/bowtie2:2.3.4--py36pl5.22.0_0"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin "$((Math.ceil(3 * (function(size_of=0){inputs.fasta_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1000^3 < 1 ? 1 : (function(size_of=0){inputs.fasta_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1000^3) ) * 1024)" ;
ResourceRequirement:ramMin 6.67572e+03
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/bowtie2:2.3.4--py36pl5.22.0_0"
] ;
cwl:inputs , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\n# if the WDL/task contains a monitoring script as input\nif [ ! -z \"$(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path)\" ]; then\n chmod a+x $(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path)\n $(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path) > monitoring.log &\nelse\n echo \"No monitoring script given as input\" > monitoring.log &\nfi\n\nbowtie2-build \\\n -f $(inputs.fasta_input.path) $(inputs.index_prefix)\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\n# if the WDL/task contains a monitoring script as input\nif [ ! -z \"$(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path)\" ]; then\n chmod a+x $(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path)\n $(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path) > monitoring.log &\nelse\n echo \"No monitoring script given as input\" > monitoring.log &\nfi\n\nbowtie2-build \\\n -f $(inputs.fasta_input.path) $(inputs.index_prefix)\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
sld:default "BS_GA" .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.index_prefix + \"*\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.index_prefix + \"*\")" ] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] ;
sld:type [ sld:items cwl:File ;
sld:type sld:array
] .
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(\"genome_mfa.GA_conversion.fa\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(\"genome_mfa.GA_conversion.fa\")" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"monitoring.log" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"monitoring.log" ] ;
sld:type cwl:File .
cwl:source .
sld:type cwl:File .
sld:type cwl:File .
cwl:source .
cwl:outputSource ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
sld:type cwl:File , sld:null .
sld:default "1.0.0" ;
sld:type xsd:string .
a cwl:Workflow ;
ns1:original_cwlVersion "v1.2" ;
Workflow:steps , , , , ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , , ;
cwl:outputs , , , , , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
sld:type cwl:File , sld:null .
sld:type cwl:File , sld:null .
cwl:outputBinding [ CommandOutputBinding:glob
"monitoring.log" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"monitoring.log" ] ;
sld:type cwl:File .
a cwl:CommandLineTool ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin "$((Math.ceil(3 * (function(size_of=0){inputs.fasta_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1000^3 < 1 ? 1 : (function(size_of=0){inputs.fasta_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1000^3) ) * 1024)" ;
ResourceRequirement:ramMin 6.67572e+03
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/bowtie2:2.3.4--py36pl5.22.0_0"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/bowtie2:2.3.4--py36pl5.22.0_0"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin "$((Math.ceil(3 * (function(size_of=0){inputs.fasta_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1000^3 < 1 ? 1 : (function(size_of=0){inputs.fasta_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1000^3) ) * 1024)" ;
ResourceRequirement:ramMin 6.67572e+03
] ;
cwl:inputs , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\n# if the WDL/task contains a monitoring script as input\nif [ ! -z \"$(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path)\" ]; then\n chmod a+x $(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path)\n $(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path) > monitoring.log &\nelse\n echo \"No monitoring script given as input\" > monitoring.log &\nfi\n\nbowtie2-build \\\n -f $(inputs.fasta_input.path) $(inputs.index_prefix)\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\n# if the WDL/task contains a monitoring script as input\nif [ ! -z \"$(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path)\" ]; then\n chmod a+x $(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path)\n $(inputs.monitoring_script === null ? \"\" : inputs.monitoring_script.path) > monitoring.log &\nelse\n echo \"No monitoring script given as input\" > monitoring.log &\nfi\n\nbowtie2-build \\\n -f $(inputs.fasta_input.path) $(inputs.index_prefix)\n" ;
cwl:entryname "script.bash"
]
] .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.reference_fasta.basename.replace(/\\.fa$/, '') .split('/').reverse()[0].replace(/\\.fasta$/, '') + \".dict\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.reference_fasta.basename.replace(/\\.fa$/, '') .split('/').reverse()[0].replace(/\\.fasta$/, '') + \".dict\")" ] ;
sld:type cwl:File .
sld:type cwl:File , sld:null .
cwl:source .