@prefix NetworkAccess: .
@prefix rdf: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix Workflow: .
@prefix cwl: .
@prefix sld: .
@prefix rdfs: .
@prefix ResourceRequirement: .
@prefix CommandOutputBinding: .
@prefix ns1: .
@prefix ExpressionTool: .
cwl:in ;
cwl:out ;
cwl:run [ a cwl:ExpressionTool ;
ExpressionTool:expression "${return {\"annotation_gtf\": inputs.target}; }" ;
cwl:inputs ;
cwl:outputs
] .
rdfs:comment "the actual number of gencode, ex. 27" ;
sld:type xsd:string .
cwl:source .
sld:type sld:Any .
cwl:outputSource ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(\"rsem_primary_gencode_\" + inputs.organism + \"_v\" + inputs.gtf_version + \".tar\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(\"rsem_primary_gencode_\" + inputs.organism + \"_v\" + inputs.gtf_version + \".tar\")" ] ;
sld:type cwl:File .
sld:type sld:Any .
sld:fields , ;
sld:type sld:record .
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:outputEval
"$({ \"genome_fa\": { \"class\": \"File\", \"path\": runtime.outdir+\"/\"+\"modified_GRC\" + inputs.organism_prefix + \"38.primary_assembly.genome.fa\" }, \"annotation_gtf\": { \"class\": \"File\", \"path\": runtime.outdir+\"/\"+\"modified_gencode.v\" + inputs.gtf_version + \".primary_assembly.annotation.gtf\" } })" ] ;
cwl:outputBinding [ CommandOutputBinding:outputEval
"$({ \"genome_fa\": { \"class\": \"File\", \"path\": runtime.outdir+\"/\"+\"modified_GRC\" + inputs.organism_prefix + \"38.primary_assembly.genome.fa\" }, \"annotation_gtf\": { \"class\": \"File\", \"path\": runtime.outdir+\"/\"+\"modified_gencode.v\" + inputs.gtf_version + \".primary_assembly.annotation.gtf\" } })" ] ;
sld:type .
sld:type xsd:string .
sld:type .
cwl:in ;
cwl:out ;
cwl:run [ a cwl:ExpressionTool ;
ExpressionTool:expression "${return {\"genome_fa\": inputs.target}; }" ;
cwl:inputs ;
cwl:outputs
] .
cwl:in , , ;
cwl:out ;
cwl:run .
cwl:source ;
cwl:valueFrom "$(self.genome_fa)" .
cwl:source ;
cwl:valueFrom "$(self.genome_fa)" .
sld:type xsd:string .
sld:type xsd:string .
sld:type cwl:File .
sld:fields , ;
sld:type sld:record .
cwl:outputSource ;
sld:type cwl:File .
sld:type xsd:string .
cwl:outputSource ;
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:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/humancellatlas/secondary-analysis-umitools:0.0.1"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 8 ;
ResourceRequirement:outdirMin 102400 ;
ResourceRequirement:ramMin 8.192e+03
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/humancellatlas/secondary-analysis-umitools:0.0.1"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 8 ;
ResourceRequirement:outdirMin 102400 ;
ResourceRequirement:ramMin 8.192e+03
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
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 "\nset -exo pipefail\n\n\n# index the fasta file\n\nmkdir genome_fa\nln -s $(inputs.references.genome_fa.path) genome_fa/$(inputs.references.genome_fa.basename)\nsamtools faidx genome_fa/$(inputs.references.genome_fa.basename)\ncut -f1,2 genome_fa/$(inputs.references.genome_fa.basename).fai > sizes.genome\n\nawk -F '\\t' '{ printf \"@SQ\\tSN:%s\\tLN:%s\\n\", $1, $2 }' sizes.genome >> $(inputs.references.annotation_gtf.basename.replace(/\\.gtf$/, '') + \".interval_list\")\n\ngrep 'gene_type \"rRNA\"' $(inputs.references.annotation_gtf.path) |\n awk '$3 == \"transcript\"' |\ncut -f1,4,5,7,9 |\nperl -lane '\n /transcript_id \"([^\"]+)\"/ or die \"no transcript_id on $.\";\n print join \"\\t\", (@F[0,1,2,3], $1)\n' |\nsort -k1V -k2n -k3n >> $(inputs.references.annotation_gtf.basename.replace(/\\.gtf$/, '') + \".interval_list\")\n\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nset -exo pipefail\n\n\n# index the fasta file\n\nmkdir genome_fa\nln -s $(inputs.references.genome_fa.path) genome_fa/$(inputs.references.genome_fa.basename)\nsamtools faidx genome_fa/$(inputs.references.genome_fa.basename)\ncut -f1,2 genome_fa/$(inputs.references.genome_fa.basename).fai > sizes.genome\n\nawk -F '\\t' '{ printf \"@SQ\\tSN:%s\\tLN:%s\\n\", $1, $2 }' sizes.genome >> $(inputs.references.annotation_gtf.basename.replace(/\\.gtf$/, '') + \".interval_list\")\n\ngrep 'gene_type \"rRNA\"' $(inputs.references.annotation_gtf.path) |\n awk '$3 == \"transcript\"' |\ncut -f1,4,5,7,9 |\nperl -lane '\n /transcript_id \"([^\"]+)\"/ or die \"no transcript_id on $.\";\n print join \"\\t\", (@F[0,1,2,3], $1)\n' |\nsort -k1V -k2n -k3n >> $(inputs.references.annotation_gtf.basename.replace(/\\.gtf$/, '') + \".interval_list\")\n\n" ;
cwl:entryname "script.bash"
]
] .
sld:type cwl:File .
sld:type cwl:File .
sld:type .
cwl:outputSource ;
sld:type cwl:File .
sld:fields , ;
sld:type sld:record .
sld:type cwl:File .
cwl:source .
a cwl:CommandLineTool ;
rdfs:comment "Modify gtf files and build reference index files for STAR aligner" ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 16 ;
ResourceRequirement:outdirMin 102400 ;
ResourceRequirement:ramMin 5.12e+04
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 16 ;
ResourceRequirement:outdirMin 102400 ;
ResourceRequirement:ramMin 5.12e+04
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/humancellatlas/snss2-indices:1.1.0"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/humancellatlas/snss2-indices:1.1.0"
] ;
cwl:inputs , , , ;
cwl:outputs , , ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nset -exo pipefail\n\nbash -ex /script/modify_gtf_$(inputs.organism).sh $(inputs.references.genome_fa.path) $(inputs.references.annotation_gtf.path)\n\nmkdir star\nSTAR --runMode genomeGenerate \\\n--genomeDir star \\\n--genomeFastaFiles $(\"modified_GRC\" + inputs.organism_prefix + \"38.primary_assembly.genome.fa\") \\\n--sjdbGTFfile $(\"modified_gencode.v\" + inputs.gtf_version + \".primary_assembly.annotation.gtf\") \\\n--sjdbOverhang 100 \\\n--runThreadN 16\n\ntar -cvf $(\"modified_\" + \"star_primary_gencode_\" + inputs.organism + \"_v\" + inputs.gtf_version + \".tar\") star\n\npython3 /script/add-introns-to-gtf.py --input-gtf $(\"modified_gencode.v\" + inputs.gtf_version + \".primary_assembly.annotation.gtf\") --output-gtf $(\"introns_modified_gencode.v\" + inputs.gtf_version + \".primary_assembly.annotation.gtf\")\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nset -exo pipefail\n\nbash -ex /script/modify_gtf_$(inputs.organism).sh $(inputs.references.genome_fa.path) $(inputs.references.annotation_gtf.path)\n\nmkdir star\nSTAR --runMode genomeGenerate \\\n--genomeDir star \\\n--genomeFastaFiles $(\"modified_GRC\" + inputs.organism_prefix + \"38.primary_assembly.genome.fa\") \\\n--sjdbGTFfile $(\"modified_gencode.v\" + inputs.gtf_version + \".primary_assembly.annotation.gtf\") \\\n--sjdbOverhang 100 \\\n--runThreadN 16\n\ntar -cvf $(\"modified_\" + \"star_primary_gencode_\" + inputs.organism + \"_v\" + inputs.gtf_version + \".tar\") star\n\npython3 /script/add-introns-to-gtf.py --input-gtf $(\"modified_gencode.v\" + inputs.gtf_version + \".primary_assembly.annotation.gtf\") --output-gtf $(\"introns_modified_gencode.v\" + inputs.gtf_version + \".primary_assembly.annotation.gtf\")\n" ;
cwl:entryname "script.bash"
]
] .
sld:type xsd:string .
rdfs:comment "Either 'human' or 'mouse'" ;
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"$(\"introns_modified_gencode.v\" + inputs.gtf_version + \".primary_assembly.annotation.gtf\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(\"introns_modified_gencode.v\" + inputs.gtf_version + \".primary_assembly.annotation.gtf\")" ] ;
sld:type cwl:File .
a cwl:Workflow ;
ns1:original_cwlVersion "v1.2" ;
Workflow:steps , , , , , , , , , , , , ;
cwl:cwlVersion cwl:v1.2 ;
cwl:inputs , , , , , ;
cwl:outputs , , , , , , , , , , , , ;
cwl:requirements [ a cwl:StepInputExpressionRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:in ;
cwl:out ;
cwl:run .
sld:type xsd:string .
sld:type cwl:File .
sld:type .
cwl:source ;
cwl:valueFrom "$(self.annotation_gtf)" .
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 8 ;
ResourceRequirement:outdirMin 102400 ;
ResourceRequirement:ramMin 8.192e+03
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/humancellatlas/secondary-analysis-hisat2:v0.2.2-2-2.1.0"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 8 ;
ResourceRequirement:outdirMin 102400 ;
ResourceRequirement:ramMin 8.192e+03
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/humancellatlas/secondary-analysis-hisat2:v0.2.2-2-2.1.0"
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\n\n# extract rsem index\ntar -xf $(inputs.rsem_index.path)\n\n# build index\nhisat2-build -p 8 rsem/rsem_trans_index.idx.fa $(\"hisat2_from_rsem_\" + inputs.rsem_index.basename.replace(/\\.tar$/, '') )\nmkdir $(\"hisat2_from_rsem_\" + inputs.rsem_index.basename.replace(/\\.tar$/, '') )\nmv ./*.ht2 $(\"hisat2_from_rsem_\" + inputs.rsem_index.basename.replace(/\\.tar$/, '') )\ntar -zcvf $(\"hisat2_from_rsem_\" + inputs.rsem_index.basename.replace(/\\.tar$/, '') + \".tar.gz\") $(\"hisat2_from_rsem_\" + inputs.rsem_index.basename.replace(/\\.tar$/, '') )\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\n\n# extract rsem index\ntar -xf $(inputs.rsem_index.path)\n\n# build index\nhisat2-build -p 8 rsem/rsem_trans_index.idx.fa $(\"hisat2_from_rsem_\" + inputs.rsem_index.basename.replace(/\\.tar$/, '') )\nmkdir $(\"hisat2_from_rsem_\" + inputs.rsem_index.basename.replace(/\\.tar$/, '') )\nmv ./*.ht2 $(\"hisat2_from_rsem_\" + inputs.rsem_index.basename.replace(/\\.tar$/, '') )\ntar -zcvf $(\"hisat2_from_rsem_\" + inputs.rsem_index.basename.replace(/\\.tar$/, '') + \".tar.gz\") $(\"hisat2_from_rsem_\" + inputs.rsem_index.basename.replace(/\\.tar$/, '') )\n" ;
cwl:entryname "script.bash"
]
] .
cwl:outputSource ;
sld:type cwl:File .
cwl:in , , ;
cwl:out ;
cwl:run .
sld:type sld:Any .
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(\"star_primary_gencode_\" + inputs.organism + \"_v\" + inputs.gtf_version + \".tar.gz\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(\"star_primary_gencode_\" + inputs.organism + \"_v\" + inputs.gtf_version + \".tar.gz\")" ] ;
sld:type cwl:File .
sld:type .
sld:fields , ;
sld:type sld:record .
cwl:in ;
cwl:out ;
cwl:run .
cwl:outputSource ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:outputEval
"$({ \"genome_fa\": { \"class\": \"File\", \"path\": runtime.outdir+\"/\"+\"GRC\" + inputs.organism_prefix + \"38.primary_assembly.genome.fa\" }, \"annotation_gtf\": { \"class\": \"File\", \"path\": runtime.outdir+\"/\"+\"gencode.v\" + inputs.gtf_version + \".primary_assembly.annotation.gtf\" } })" ] ;
cwl:outputBinding [ CommandOutputBinding:outputEval
"$({ \"genome_fa\": { \"class\": \"File\", \"path\": runtime.outdir+\"/\"+\"GRC\" + inputs.organism_prefix + \"38.primary_assembly.genome.fa\" }, \"annotation_gtf\": { \"class\": \"File\", \"path\": runtime.outdir+\"/\"+\"gencode.v\" + inputs.gtf_version + \".primary_assembly.annotation.gtf\" } })" ] ;
sld:type .
sld:type xsd:string .
cwl:outputSource ;
sld:type cwl:File .
sld:fields , ;
sld:type sld:record .
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
a cwl:CommandLineTool ;
rdfs:comment "build reference index files for STAR aligner" ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 16 ;
ResourceRequirement:outdirMin 102400 ;
ResourceRequirement:ramMin 5.12e+04
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/humancellatlas/secondary-analysis-star:v2.7.9a"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/humancellatlas/secondary-analysis-star:v2.7.9a"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 16 ;
ResourceRequirement:outdirMin 102400 ;
ResourceRequirement:ramMin 5.12e+04
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nset -exo pipefail\n\nmkdir star\nSTAR --runMode genomeGenerate \\\n --genomeDir star \\\n --genomeFastaFiles $(inputs.references.genome_fa.path) \\\n --sjdbGTFfile $(inputs.references.annotation_gtf.path) \\\n --sjdbOverhang 100 \\\n --runThreadN 16\n\ntar -cvf $(\"star_primary_gencode_\" + inputs.organism + \"_v\" + inputs.gtf_version + \".tar\") star\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 "\nset -exo pipefail\n\nmkdir star\nSTAR --runMode genomeGenerate \\\n --genomeDir star \\\n --genomeFastaFiles $(inputs.references.genome_fa.path) \\\n --sjdbGTFfile $(inputs.references.annotation_gtf.path) \\\n --sjdbOverhang 100 \\\n --runThreadN 16\n\ntar -cvf $(\"star_primary_gencode_\" + inputs.organism + \"_v\" + inputs.gtf_version + \".tar\") star\n" ;
cwl:entryname "script.bash"
]
] .
cwl:outputBinding [ CommandOutputBinding:glob
"$(\"hisat2_from_rsem_\" + inputs.rsem_index.basename.replace(/\\.tar$/, '') + \".tar.gz\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(\"hisat2_from_rsem_\" + inputs.rsem_index.basename.replace(/\\.tar$/, '') + \".tar.gz\")" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(\"modified_\" + \"star_primary_gencode_\" + inputs.organism + \"_v\" + inputs.gtf_version + \".tar\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(\"modified_\" + \"star_primary_gencode_\" + inputs.organism + \"_v\" + inputs.gtf_version + \".tar\")" ] ;
sld:type cwl:File .
sld:type xsd:string .
rdfs:comment "e.g. hg38, mm10" ;
sld:type xsd:string .
sld:type xsd:string .
sld:type cwl:File .
cwl:in ;
cwl:out ;
cwl:run [ a cwl:ExpressionTool ;
ExpressionTool:expression "${return {\"genome_fa\": inputs.target}; }" ;
cwl:inputs ;
cwl:outputs
] .
cwl:source .
sld:type cwl:File .
cwl:in , , , , ;
cwl:out ;
cwl:run .
cwl:source ;
cwl:valueFrom "$(self.genome_fa)" .
sld:type xsd:string .
a cwl:CommandLineTool ;
rdfs:comment "build reference index files for RSEM" ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:outdirMin 102400 ;
ResourceRequirement:ramMin 1.024e+04
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/humancellatlas/secondary-analysis-rsem:v0.2.2-1.3.0"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:outdirMin 102400 ;
ResourceRequirement:ramMin 1.024e+04
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/humancellatlas/secondary-analysis-rsem:v0.2.2-1.3.0"
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nset -eo pipefail\nmkdir rsem\nrsem-prepare-reference --gtf $(inputs.references.annotation_gtf.path) --bowtie $(inputs.references.genome_fa.path) rsem/rsem_trans_index\ntar -cvf $(\"rsem_primary_gencode_\" + inputs.organism + \"_v\" + inputs.gtf_version + \".tar\") rsem/\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nset -eo pipefail\nmkdir rsem\nrsem-prepare-reference --gtf $(inputs.references.annotation_gtf.path) --bowtie $(inputs.references.genome_fa.path) rsem/rsem_trans_index\ntar -cvf $(\"rsem_primary_gencode_\" + inputs.organism + \"_v\" + inputs.gtf_version + \".tar\") rsem/\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:source .
sld:type xsd:string .
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 "quay.io/humancellatlas/gtf_to_genepred:v0.0.0"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/humancellatlas/gtf_to_genepred:v0.0.0"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 8 ;
ResourceRequirement:outdirMin 102400 ;
ResourceRequirement:ramMin 8.192e+03
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 8 ;
ResourceRequirement:outdirMin 102400 ;
ResourceRequirement:ramMin 8.192e+03
] ;
cwl:inputs ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nset -eo pipefail\n\ngtfToGenePred -genePredExt -geneNameAsName2 $(inputs.references.annotation_gtf.path) refflat.tmp.txt\n\npaste <(cut -f 12 refflat.tmp.txt) <(cut -f 1-10 refflat.tmp.txt) > $(inputs.references.annotation_gtf.basename.replace(/\\.gtf$/, '') + \".refflat.txt\")\n\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nset -eo pipefail\n\ngtfToGenePred -genePredExt -geneNameAsName2 $(inputs.references.annotation_gtf.path) refflat.tmp.txt\n\npaste <(cut -f 12 refflat.tmp.txt) <(cut -f 1-10 refflat.tmp.txt) > $(inputs.references.annotation_gtf.basename.replace(/\\.gtf$/, '') + \".refflat.txt\")\n\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
sld:type xsd:string .
a cwl:CommandLineTool ;
rdfs:comment "Download files needed for building the designated references" ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:outdirMin 10240
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/humancellatlas/secondary-analysis-star:v2.7.9a"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:outdirMin 10240
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/humancellatlas/secondary-analysis-star:v2.7.9a"
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nset -exo pipefail\n\n## download fasta\nwget $(\"ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_\" + inputs.organism + \"/release_\" + inputs.gtf_version)/$(\"GRC\" + inputs.organism_prefix + \"38.primary_assembly.genome.fa\").gz\ngunzip $(\"GRC\" + inputs.organism_prefix + \"38.primary_assembly.genome.fa\").gz\n\n## download gtf file\nwget $(\"ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_\" + inputs.organism + \"/release_\" + inputs.gtf_version)/$(\"gencode.v\" + inputs.gtf_version + \".primary_assembly.annotation.gtf\").gz\ngunzip $(\"gencode.v\" + inputs.gtf_version + \".primary_assembly.annotation.gtf\").gz\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 "\nset -exo pipefail\n\n## download fasta\nwget $(\"ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_\" + inputs.organism + \"/release_\" + inputs.gtf_version)/$(\"GRC\" + inputs.organism_prefix + \"38.primary_assembly.genome.fa\").gz\ngunzip $(\"GRC\" + inputs.organism_prefix + \"38.primary_assembly.genome.fa\").gz\n\n## download gtf file\nwget $(\"ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_\" + inputs.organism + \"/release_\" + inputs.gtf_version)/$(\"gencode.v\" + inputs.gtf_version + \".primary_assembly.annotation.gtf\").gz\ngunzip $(\"gencode.v\" + inputs.gtf_version + \".primary_assembly.annotation.gtf\").gz\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] .
cwl:in , , ;
cwl:out ;
cwl:run .
sld:type xsd:string .
sld:type cwl:File .
cwl:source .
cwl:in ;
cwl:out ;
cwl:run .
cwl:outputSource ;
sld:type cwl:File .
sld:default "0.1.1" ;
sld:type xsd:string .
cwl:source .
cwl:source .
sld:type xsd:string .
cwl:in , , , ;
cwl:out , , ;
cwl:run .
cwl:source .
cwl:in ;
cwl:out ;
cwl:run [ a cwl:ExpressionTool ;
ExpressionTool:expression "${return {\"annotation_gtf\": inputs.target}; }" ;
cwl:inputs ;
cwl:outputs
] .
sld:type xsd:string .
cwl:outputSource