@prefix NetworkAccess: .
@prefix rdf: .
@prefix xsd: .
@prefix DockerRequirement: .
@prefix cwl: .
@prefix Workflow: .
@prefix ResourceRequirement: .
@prefix sld: .
@prefix rdfs: .
@prefix CommandOutputBinding: .
@prefix ns1: .
rdfs:comment "base name to be used for the output of the task" ;
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"$('output/binCoordinates_' + inputs.bin_size_list + '.csv')" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$('output/binCoordinates_' + inputs.bin_size_list + '.csv')" ] ;
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/humancellatlas/snap-breakout:0.0.1"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin "$(1)" ;
ResourceRequirement:outdirMin "$((Math.ceil(10 * (function(size_of=0){inputs.snap_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 < 1 ? 1 : (function(size_of=0){inputs.snap_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3) ) * 1024)" ;
ResourceRequirement:ramMin 1.525879e+04
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin "$(1)" ;
ResourceRequirement:outdirMin "$((Math.ceil(10 * (function(size_of=0){inputs.snap_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 < 1 ? 1 : (function(size_of=0){inputs.snap_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3) ) * 1024)" ;
ResourceRequirement:ramMin 1.525879e+04
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/humancellatlas/snap-breakout:0.0.1"
] ;
cwl:inputs , , ;
cwl:outputs , , , , ;
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 -euo pipefail\nmkdir output\nbreakoutSnap.py --input $(inputs.snap_input.path) \\\n --output-prefix output/\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nset -euo pipefail\nmkdir output\nbreakoutSnap.py --input $(inputs.snap_input.path) \\\n --output-prefix output/\n" ;
cwl:entryname "script.bash"
]
] .
cwl:source .
cwl:in , , ;
cwl:out , , , , ;
cwl:run .
rdfs:comment "the bam to be sorted by picard tools" ;
sld:type cwl:File .
cwl:source .
sld:default "coordinate" ;
sld:type xsd:string .
cwl:source .
cwl:source .
sld:default "quay.io/humancellatlas/snap-breakout:0.0.1" ;
sld:type xsd:string .
cwl:source .
rdfs:comment "the name of the genome being analyzed" ;
sld:type xsd:string .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_base_name + \".aligned.sam\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_base_name + \".aligned.sam\")" ] ;
sld:type cwl:File .
rdfs:comment "the desired way for the bam to be sorted (default: coordinate)" ;
sld:default "coordinate" ;
sld:type xsd:string .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"monitoring.log" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"monitoring.log" ] ;
sld:type cwl:File , sld:null .
a cwl:CommandLineTool ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/humancellatlas/snaptools:0.0.1"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/humancellatlas/snaptools:0.0.1"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin "$((Math.ceil(2.5 * (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 < 1 ? 1 : (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3) ) * 1024)" ;
ResourceRequirement:ramMin 4.096e+03
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin "$((Math.ceil(2.5 * (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 < 1 ? 1 : (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3) ) * 1024)" ;
ResourceRequirement:ramMin 4.096e+03
] ;
cwl:inputs , , ;
cwl:outputs ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nmakeCompliantBAM.py \\\n --input-bam $(inputs.bam_input.path) \\\n --output-bam $(inputs.output_base_name + \".compliant.bam\")\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nmakeCompliantBAM.py \\\n --input-bam $(inputs.bam_input.path) \\\n --output-bam $(inputs.output_base_name + \".compliant.bam\")\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] .
rdfs:comment "read 2 fastq file as input for the pipeline" ;
sld:type cwl:File .
rdfs:comment "the read group id to be added upon alignment" ;
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_base_name + \".sorted.\" + inputs.sort_order + \".bam\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_base_name + \".sorted.\" + inputs.sort_order + \".bam\")" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:in , , , , , , , ;
cwl:out , ;
cwl:run .
sld:default "quay.io/biocontainers/picard:2.18.3--py27_0" ;
sld:type xsd:string .
rdfs:comment "the docker image using picard to be used (default: quay.io/biocontainers/picard:2.18.3--py27_0)" ;
sld:default "quay.io/biocontainers/picard:2.18.3--py27_0" ;
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_base_name + \".compliant.bam\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_base_name + \".compliant.bam\")" ] ;
sld:type cwl:File .
rdfs:comment "the pre built tar file containing the reference fasta and corresponding reference files for the BWA aligner" ;
sld:type cwl:File .
cwl:source .
cwl:source .
sld:default "quay.io/humancellatlas/snaptools:0.0.1" ;
sld:type xsd:string .
rdfs:comment "the minimum legnth for trimming. Reads that are too short even before adapter removal are also discarded" ;
sld:type xsd:int .
cwl:in , , , ;
cwl:out , ;
cwl:run .
cwl:source .
rdfs:comment "base name to be used for the output of the task" ;
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.snap_output_name)" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.snap_output_name)" ] ;
sld:type cwl:File .
rdfs:comment "name of the file with chromosome sizes for the genome in the input tar file" ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_base_name + \".snap\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_base_name + \".snap\")" ] ;
sld:type cwl:File .
cwl:in , , , ;
cwl:out , ;
cwl:run .
rdfs:comment "the read group sample to be added upon alignment" ;
sld:default "RGSN1" ;
sld:type xsd:string .
a cwl:CommandLineTool ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/humancellatlas/snaptools:0.0.1"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin "$((Math.ceil(2.5 * (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 < 1 ? 1 : (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3) ) * 1024)" ;
ResourceRequirement:ramMin 4.096e+03
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin "$((Math.ceil(2.5 * (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 < 1 ? 1 : (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3) ) * 1024)" ;
ResourceRequirement:ramMin 4.096e+03
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/humancellatlas/snaptools:0.0.1"
] ;
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:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nmakeCompliantBAM.py \\\n --input-bam $(inputs.bam_input.path) \\\n --output-bam $(inputs.output_base_name + \".compliant.bam\")\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nmakeCompliantBAM.py \\\n --input-bam $(inputs.bam_input.path) \\\n --output-bam $(inputs.output_base_name + \".compliant.bam\")\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:source .
rdfs:comment "base name to be used for the output of the task" ;
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"monitoring.log" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"monitoring.log" ] ;
sld:type cwl:File , sld:null .
cwl:source .
cwl:source .
sld:default "quay.io/biocontainers/samtools:1.9--h10a08f8_12" ;
sld:type xsd:string .
sld:default "quay.io/biocontainers/samtools:1.9--h10a08f8_12" ;
sld:type xsd:string .
cwl:source .
rdfs:comment "the bam with barcodes in the read ids that need to be converted to barcodes in bam tags" ;
sld:type cwl:File .
a cwl:CommandLineTool ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin "$((Math.ceil(2 * (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 < 1 ? 1 : (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3) ) * 1024)" ;
ResourceRequirement:ramMin 3.84e+03
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/samtools:1.9--h10a08f8_12"
] ;
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 "$((Math.ceil(2 * (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 < 1 ? 1 : (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3) ) * 1024)" ;
ResourceRequirement:ramMin 3.84e+03
] ;
cwl:inputs , , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nset -euo pipefail\n\n# filter for a map quality\n# -b output is bam, -h include header, -q reads with mapping quality >=\nsamtools view \\\n -bh \\\n -q$(inputs.min_map_quality) \\\n $(inputs.bam_input.path) \\\n > $(inputs.output_base_name + \".filtered.min_map_quality.bam\")\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nset -euo pipefail\n\n# filter for a map quality\n# -b output is bam, -h include header, -q reads with mapping quality >=\nsamtools view \\\n -bh \\\n -q$(inputs.min_map_quality) \\\n $(inputs.bam_input.path) \\\n > $(inputs.output_base_name + \".filtered.min_map_quality.bam\")\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_base_name + \".bam\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_base_name + \".bam\")" ] ;
sld:type cwl:File .
rdfs:comment "the bam to passed into snaptools tools" ;
sld:type cwl:File .
cwl:in , , ;
cwl:out ;
cwl:run .
rdfs:comment "cutadapt option for the sequence adapter for read 1 fastq" ;
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"output/fragments.csv" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"output/fragments.csv" ] ;
sld:type cwl:File .
cwl:source .
rdfs:comment "the bam to passed into snaptools tools" ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"output/barcodesSection.csv" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"output/barcodesSection.csv" ] ;
sld:type cwl:File .
cwl:outputSource ;
sld:type cwl:File .
cwl:source .
cwl:source .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"monitoring.log" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"monitoring.log" ] ;
sld:type cwl:File , sld:null .
cwl:source .
rdfs:comment "base name to be used for the output of the task" ;
sld:type xsd:string .
rdfs:comment "base name to be used for the output of the task" ;
sld:type xsd:string .
rdfs:comment "the docker image using snaptools to be used (default: quay.io/humancellatlas/snaptools:0.0.1)" ;
sld:default "quay.io/humancellatlas/snaptools:0.0.1" ;
sld:type xsd:string .
a cwl:CommandLineTool ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin "$(inputs.cpu)" ;
ResourceRequirement:outdirMin "$((Math.ceil(3.25 * (function(size_of=0){inputs.fastq_input_read1.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 + (function(size_of=0){inputs.fastq_input_read2.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 + (function(size_of=0){inputs.tar_bwa_reference.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 < 1 ? 1 : (function(size_of=0){inputs.fastq_input_read1.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 + (function(size_of=0){inputs.fastq_input_read2.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 + (function(size_of=0){inputs.tar_bwa_reference.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3) ) * 1024)" ;
ResourceRequirement:ramMin 3.84e+03
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/humancellatlas/snaptools:0.0.1"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/humancellatlas/snaptools:0.0.1"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin "$(inputs.cpu)" ;
ResourceRequirement:outdirMin "$((Math.ceil(3.25 * (function(size_of=0){inputs.fastq_input_read1.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 + (function(size_of=0){inputs.fastq_input_read2.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 + (function(size_of=0){inputs.tar_bwa_reference.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 < 1 ? 1 : (function(size_of=0){inputs.fastq_input_read1.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 + (function(size_of=0){inputs.fastq_input_read2.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 + (function(size_of=0){inputs.tar_bwa_reference.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3) ) * 1024)" ;
ResourceRequirement:ramMin 3.84e+03
] ;
cwl:inputs , , , , , , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nset -euo pipefail\n\n# prepare reference\ndeclare -r REF_DIR=\\$(mktemp -d genome_referenceXXXXXX)\ntar -xf \"$(inputs.tar_bwa_reference.path)\" -C $REF_DIR --strip-components 1\nrm \"$(inputs.tar_bwa_reference.path)\" || /bin/true\n\n# align w/ BWA: -t for number of cores\nbwa \\\n mem \\\n -R \"@RG\\tID:$(inputs.read_group_id)\\tSM:$(inputs.read_group_sample_name)\" \\\n -t $(inputs.cpu) \\\n $REF_DIR/genome.fa \\\n <(zcat $(inputs.fastq_input_read1.path)) <(zcat $(inputs.fastq_input_read2.path)) \\\n > $(inputs.output_base_name + \".aligned.sam\")\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nset -euo pipefail\n\n# prepare reference\ndeclare -r REF_DIR=\\$(mktemp -d genome_referenceXXXXXX)\ntar -xf \"$(inputs.tar_bwa_reference.path)\" -C $REF_DIR --strip-components 1\nrm \"$(inputs.tar_bwa_reference.path)\" || /bin/true\n\n# align w/ BWA: -t for number of cores\nbwa \\\n mem \\\n -R \"@RG\\tID:$(inputs.read_group_id)\\tSM:$(inputs.read_group_sample_name)\" \\\n -t $(inputs.cpu) \\\n $REF_DIR/genome.fa \\\n <(zcat $(inputs.fastq_input_read1.path)) <(zcat $(inputs.fastq_input_read2.path)) \\\n > $(inputs.output_base_name + \".aligned.sam\")\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
a cwl:CommandLineTool ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "broadinstitute/gatk:4.1.2.0"
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "broadinstitute/gatk:4.1.2.0"
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin "$((Math.ceil(2 * (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 < 1 ? 1 : (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3) ) * 1024)" ;
ResourceRequirement:ramMin 3.75e+03
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin "$((Math.ceil(2 * (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 < 1 ? 1 : (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3) ) * 1024)" ;
ResourceRequirement:ramMin 3.75e+03
] ;
cwl:inputs , , , ;
cwl:outputs , ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nset -euo pipefail\n\ngatk --java-options \"-Xms2750m -Xmx3250m\" \\\n PrintReads \\\n --input=$(inputs.bam_input.path) \\\n --read-filter FragmentLengthReadFilter --max-fragment-length $(inputs.max_fragment_length) \\\n --output=$(inputs.output_base_name + \".filtered.max_fragment_length.bam\")\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nset -euo pipefail\n\ngatk --java-options \"-Xms2750m -Xmx3250m\" \\\n PrintReads \\\n --input=$(inputs.bam_input.path) \\\n --read-filter FragmentLengthReadFilter --max-fragment-length $(inputs.max_fragment_length) \\\n --output=$(inputs.output_base_name + \".filtered.max_fragment_length.bam\")\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"output/barcodes.csv" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"output/barcodes.csv" ] ;
sld:type cwl:File .
rdfs:comment "the docker image using the python script to convert the bam barcodes/read ids (default: quay.io/humancellatlas/snaptools:0.0.1)" ;
sld:default "quay.io/humancellatlas/snaptools:0.0.1" ;
sld:type xsd:string .
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 "$((Math.ceil(3.25 * (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 < 1 ? 1 : (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3) ) * 1024)" ;
ResourceRequirement:ramMin 3.75e+03
] ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin "$((Math.ceil(3.25 * (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 < 1 ? 1 : (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3) ) * 1024)" ;
ResourceRequirement:ramMin 3.75e+03
] ;
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: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 "\nset -euo pipefail\n\njava -Xmx3250m -jar /usr/local/share/picard-2.18.3-0/picard.jar SortSam \\\n INPUT=$(inputs.bam_input.path) \\\n SORT_ORDER=$(inputs.sort_order) \\\n MAX_RECORDS_IN_RAM=300000 \\\n OUTPUT=$(inputs.output_base_name + \".sorted.\" + inputs.sort_order + \".bam\")\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:InitialWorkDirRequirement ;
cwl:listing [ cwl:entry "\nset -euo pipefail\n\njava -Xmx3250m -jar /usr/local/share/picard-2.18.3-0/picard.jar SortSam \\\n INPUT=$(inputs.bam_input.path) \\\n SORT_ORDER=$(inputs.sort_order) \\\n MAX_RECORDS_IN_RAM=300000 \\\n OUTPUT=$(inputs.output_base_name + \".sorted.\" + inputs.sort_order + \".bam\")\n" ;
cwl:entryname "script.bash"
]
] ;
cwl:requirements [ a cwl:NetworkAccess ;
NetworkAccess:networkAccess true
] ;
cwl:requirements [ a cwl:InlineJavascriptRequirement ] .
cwl:source .
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_base_name + \".R1.trimmed_adapters.fastq.gz\")" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"$(inputs.output_base_name + \".R1.trimmed_adapters.fastq.gz\")" ] ;
sld:type cwl:File .
cwl:outputBinding [ CommandOutputBinding:glob
"monitoring.log" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"monitoring.log" ] ;
sld:type cwl:File , sld:null .
rdfs:comment "base name to be used for the output of the task" ;
sld:type xsd:string .
cwl:source .
cwl:source .
rdfs:comment "cutadapt option to trim low-quality ends from reads before adapter removal" ;
sld:type xsd:int .
sld:default "output.snap" ;
sld:type xsd:string .
rdfs:comment "the minimum mapping quality to be filtered by samtools view and snap-pre (snaptools task)" ;
sld:type xsd:int .
rdfs:comment "base name to be used for the output of the task" ;
sld:type xsd:string .
cwl:source .
cwl:source .
rdfs:comment "the pre built tar file containing the reference fasta and cooresponding reference files for the BWA aligner" ;
sld:type cwl:File .
cwl:source .
cwl:source .
rdfs:comment "the docker image using picard to be used (default: quay.io/biocontainers/picard:2.18.3--py27_0)" ;
sld:default "quay.io/biocontainers/picard:2.18.3--py27_0" ;
sld:type xsd:string .
rdfs:comment "the desired way for the bam to be sorted (default: coordinate)" ;
sld:default "coordinate" ;
sld:type xsd:string .
cwl:in , , , , , , , ;
cwl:out , , ;
cwl:run .
rdfs:comment "base name to be used for the output of the task" ;
sld:type xsd:string .
cwl:in , , , ;
cwl:out ;
cwl:run .
rdfs:comment "the docker image to be used (default: quay.io/humancellatlas/snaptools:0.0.1)" ;
sld:default "quay.io/humancellatlas/snaptools:0.0.1" ;
sld:type xsd:string .
cwl:source .
rdfs:comment "cutadapt option for the sequence adapter for read 2 fastq" ;
sld:type xsd:string .
rdfs:comment "the bam to be sorted by picard tools" ;
sld:type cwl:File .
sld:default "queryname" .
cwl:source .
sld:default "quay.io/humancellatlas/snaptools:0.0.1" ;
sld:type xsd:string .
cwl:outputBinding [ CommandOutputBinding:glob
"monitoring.log" ] ;
cwl:outputBinding [ CommandOutputBinding:glob
"monitoring.log" ] ;
sld:type cwl:File , sld:null .
rdfs:comment "cutadapt option for the sequence adapter for read 1 fastq" ;
sld:type xsd:string .
cwl:source ;
cwl:valueFrom "$(self + \".chrM_reads\")" .
sld:type cwl:File .
rdfs:comment "the name of the genome being analyzed, input to snap tools, curently mm10 and hg19 supported" ;
sld:type xsd:string .
rdfs:comment "the aligned sam produced by the aligner" ;
sld:type cwl:File .
sld:default "quay.io/humancellatlas/snap-breakout:0.0.1" ;
sld:type xsd:string .
a cwl:CommandLineTool ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:baseCommand ( "bash" "script.bash" ) ;
cwl:cwlVersion cwl:v1.2 ;
cwl:hints [ a cwl:ResourceRequirement ;
ResourceRequirement:coresMin 1 ;
ResourceRequirement:outdirMin "$((Math.ceil(3.25 * (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 < 1 ? 1 : (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3) ) * 1024)" ;
ResourceRequirement:ramMin 3.75e+03
] ;
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(3.25 * (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3 < 1 ? 1 : (function(size_of=0){inputs.bam_input.forEach(function(element){ if (element) {size_of += element.size}})}) / 1024^3) ) * 1024)" ;
ResourceRequirement:ramMin 3.75e+03
] ;
cwl:hints [ a cwl:DockerRequirement ;
DockerRequirement:dockerPull "quay.io/biocontainers/picard:2.18.3--py27_0"
] ;
cwl:inputs , , , ;
cwl:outputs ,