@prefix LoadListingRequirement: .
@prefix CommandLineBinding: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
@prefix NetworkAccess: .
@prefix rdf: .
@prefix cwl: .
@prefix ResourceRequirement: .
cwl:outputSource ;
sld:type cwl:Directory .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.sample_name)/outs/" ] ;
sld:type cwl:Directory .
cwl:source .
cwl:source .
sld:type cwl:Directory .
cwl:source .
cwl:inputBinding [ CommandLineBinding:position
-1 ] ;
sld:type xsd:string .
cwl:default 3 ;
sld:type xsd:int , sld:null .
cwl:source .
sld:type cwl:Directory .
rdfs:comment "Transcriptome reference compatible with input species and Cell Ranger" ;
cwl:inputBinding [ CommandLineBinding:position 3 ;
CommandLineBinding:prefix "--transcriptome=" ;
CommandLineBinding:separate false
] ;
sld:type cwl:Directory .
cwl:source .
cwl:outputSource ;
sld:type cwl:Directory .
sld:type xsd:string .
a cwl:Workflow ;
rdfs:label "Running cellranger count and lineage inference" ;
ns1:original_cwlVersion "v1.0" ;
Workflow:steps , ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , , , ;
cwl:outputs , .
cwl:default 10 ;
sld:type xsd:int , sld:null .
a cwl:CommandLineTool ;
rdfs:label "Run Cell Ranger Count" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "--id=$(inputs.sample_name)" "--localcores=$(runtime.cores)" "--localmem=$(runtime.ram/1000)" ) ;
cwl:baseCommand ( "/opt/cellranger-3.0.1/cellranger" "count" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:inputs , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "registry.gsc.wustl.edu/mgi/cellranger:3.0.1"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 8 ;
ResourceRequirement:ramMin 56000
] .
cwl:inputBinding [ CommandLineBinding:position
1 ] ;
sld:type xsd:string .
rdfs:comment "Sample name, must be same as name specified in sample sheet in previous mkfastq step" ;
cwl:inputBinding [ CommandLineBinding:position 4 ;
CommandLineBinding:prefix "--sample=" ;
CommandLineBinding:separate false
] ;
sld:type xsd:string .
rdfs:comment "Array of directories containing fastq files" ;
cwl:inputBinding [ CommandLineBinding:itemSeparator
"," ;
CommandLineBinding:position 2 ;
CommandLineBinding:prefix "--fastqs=" ;
CommandLineBinding:separate false
] ;
sld:type [ sld:items cwl:Directory ;
sld:type sld:array
] .
sld:type xsd:string .
cwl:default 3 ;
cwl:inputBinding [ CommandLineBinding:position
2 ] ;
sld:type xsd:int , sld:null .
cwl:in , , , ;
cwl:out ;
cwl:run .
cwl:source .
sld:type [ sld:items cwl:Directory ;
sld:type sld:array
] .
cwl:source .
sld:type xsd:string , sld:null .
cwl:default 10 ;
cwl:inputBinding [ CommandLineBinding:position
3 ] ;
sld:type xsd:int , sld:null .
a cwl:CommandLineTool ;
rdfs:label "Running a script to identify lineage of cells" ;
ns1:original_cwlVersion "v1.0" ;
cwl:arguments ( "$(inputs.cellranger_out_dir)/filtered_feature_bc_matrix" "cellmatch" ) ;
cwl:baseCommand ( "/usr/local/bin/Rscript" "/opt/CellMatch_Haemopedia.r" ) ;
cwl:cwlVersion ;
cwl:hints [ a ;
NetworkAccess:networkAccess true
] ;
cwl:hints [ a ;
LoadListingRequirement:loadListing
"deep_listing"
] ;
cwl:inputs , , , , ;
cwl:outputs ;
cwl:requirements [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "mgibio/scrna_lineage_inference:0.2"
] ;
cwl:requirements [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:ramMin 16000
] .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"cellmatch" ] ;
sld:type cwl:Directory .
cwl:source .
rdfs:comment "Assay configuration used, default 'auto' should usually work without issue" ;
cwl:default "auto" ;
cwl:inputBinding [ CommandLineBinding:position 1 ;
CommandLineBinding:prefix "--chemistry=" ;
CommandLineBinding:separate false
] ;
sld:type xsd:string , sld:null .
cwl:in , , , , ;
cwl:out ;
cwl:run .