@prefix LoadListingRequirement: . @prefix CommandLineBinding: . @prefix xsd: . @prefix DockerRequirement: . @prefix Workflow: . @prefix sld: . @prefix rdfs: . @prefix CommandOutputBinding: . @prefix ns1: . @prefix NetworkAccess: . @prefix rdf: . @prefix ScatterMethod: . @prefix cwl: . @prefix ResourceRequirement: . cwl:source . cwl:source . sld:type xsd:int . cwl:source . a cwl:CommandLineTool ; rdfs:label "Trim FASTQ (flexbar)" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "--target" [ cwl:valueFrom "$(runtime.outdir)/trimmed_read" ] "--threads" [ cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:baseCommand ( "/opt/flexbar/flexbar" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 16000 ; ResourceRequirement:tmpdirMin 25000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/bisulfite" ] . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "I=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "markdup.bam" ] ; sld:type cwl:File . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type xsd:string . sld:type [ sld:items xsd:string ; sld:type sld:array ] . sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:position 7 ; CommandLineBinding:prefix "--reads" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "read1.fastq" ] ; sld:type cwl:File . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File . sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; rdfs:label "BAM to CRAM conversion" ; ns1:original_cwlVersion "v1.0" ; cwl:baseCommand ( "/opt/samtools/bin/samtools" "view" "-C" ) ; 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/samtools-cwl:1.0.0" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:stdout "$(inputs.bam.nameroot).cram" . sld:type cwl:File . sld:type xsd:string . cwl:inputBinding [ CommandLineBinding:position -2 ] ; sld:type cwl:File . cwl:source . cwl:in ; cwl:out ; cwl:run . cwl:in ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "Biscuit pileup" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position -9 ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:baseCommand ( "/bin/bash" "helper.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 16000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/biscuit:0.3.8" ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -eo pipefail\n\ncores=$1\nreference_fasta=\"$2\"\nbam=\"$3\"\n\n/usr/bin/biscuit pileup -q $cores -w pileup_stats.txt \"$reference_fasta\" \"$bam\" | /opt/htslib/bin/bgzip\n" ; cwl:entryname "helper.sh" ] ] ; cwl:stdout "pileup.vcf.gz" . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-T" ] ; sld:type xsd:string . cwl:in , ; cwl:out , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "cpgs.bw" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "cpgs.bed.gz" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot).cram" ] ; sld:type cwl:File . cwl:in , ; cwl:out ; cwl:run . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "trimmed_read_1.fastq" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "merged.bam" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position -2 ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 3 ; CommandLineBinding:prefix "--adapter-min-overlap" ] ; sld:type xsd:int . a cwl:Workflow ; rdfs:label "bam to trimmed fastqs and biscuit alignments" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "trimmed_read_*.fastq" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:in ; cwl:out ; cwl:run . cwl:inputBinding [ CommandLineBinding:position -4 ] ; sld:type xsd:string . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Sambamba: merge" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "$(runtime.cores)" "$(runtime.outdir)/merged.bam" ) ; cwl:baseCommand ( "/usr/bin/sambamba_merge" ) ; 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 "mgibio/bisulfite" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 8000 ] . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "--adapter-trim-end" ] ; sld:type xsd:string . sld:type xsd:string . cwl:source . cwl:inputBinding [ CommandLineBinding:position 8 ; CommandLineBinding:prefix "--reads2" ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "bedGraph to bigwig conversion" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 3 ; cwl:valueFrom "cpgs.bw" ] ) ; cwl:baseCommand ( "/usr/bin/bedGraphToBigWig" ) ; 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/bisulfite" ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 32000 ] . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "read2.fastq" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 5 ; CommandLineBinding:prefix "--max-uncalled" ] ; sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "cpgs.bedgraph" ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Biscuit dedup" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position -3 ; cwl:valueFrom "$(runtime.cores)" ] [ CommandLineBinding:position -2 ; cwl:valueFrom "$(runtime.outdir)" ] ) ; cwl:baseCommand ( "/bin/bash" "biscuit_markdup.sh" ) ; 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 "mgibio/biscuit:0.3.8" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 24000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -eou pipefail\n\ncores=$1\noutdir=\"$2\"\nbam=\"$3\"\n\n/usr/bin/biscuit markdup \"$bam\" /dev/stdout | /usr/bin/sambamba sort -t $cores -m 15G -o \"$outdir/markdup.bam\" /dev/stdin\n" ; cwl:entryname "biscuit_markdup.sh" ] ] . cwl:in , , , , , , ; cwl:out , ; cwl:run . cwl:inputBinding [ CommandLineBinding:position -1 ] ; sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "samtools index" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "cp" "$(inputs.bam.path)" "$(runtime.outdir)/$(inputs.bam.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/opt/samtools/bin/samtools" "index" "$(inputs.bam.path)" "$(runtime.outdir)/$(inputs.bam.basename).bai" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "ln" "-s" "$(inputs.bam.basename).bai" "$(runtime.outdir)/$(inputs.bam.nameroot).bai" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] . cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--adapters" ] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.cram.basename)" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "trimmed_read_2.fastq" ] ; sld:type cwl:File . cwl:source . cwl:source . cwl:in ; cwl:out , ; cwl:run . cwl:in , ; cwl:out ; cwl:run . a cwl:CommandLineTool ; rdfs:label "Picard: BAM to FASTQ" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "F=$(runtime.outdir)/read1.fastq" ] [ cwl:valueFrom "F2=$(runtime.outdir)/read2.fastq" ] ) ; cwl:baseCommand ( "/usr/bin/java" "-Xmx4g" "-jar" "/opt/picard/picard.jar" "SamToFastq" "VALIDATION_STRINGENCY=SILENT" ) ; 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/rnaseq" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 6000 ; ResourceRequirement:tmpdirMin 25000 ] . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "pileup.vcf.gz" ] ; sld:type cwl:File . sld:type xsd:int . cwl:in , , , , , , , ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . sld:type xsd:int . sld:type xsd:string . cwl:source . cwl:source . sld:type cwl:File . sld:type cwl:File . a cwl:CommandLineTool ; rdfs:label "Biscuit: align" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position -9 ; cwl:valueFrom "$(runtime.cores)" ] [ CommandLineBinding:position -8 ; cwl:valueFrom "$(runtime.outdir)" ] ) ; cwl:baseCommand ( "/bin/bash" "biscuit_align.sh" ) ; 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/biscuit:0.3.8" ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 12 ; ResourceRequirement:ramMin 32000 ] ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -eou pipefail\n\ncores=$1\noutdir=\"$2\"\nread_group_id=\"$3\"\nreference_index=\"$4\"\nfastq1=\"$5\"\nfastq2=\"$6\"\n\n/usr/bin/biscuit align -t $cores -M -R \"$read_group_id\" \"$reference_index\" \"$fastq1\" \"$fastq2\" | /usr/bin/sambamba view -S -f bam -l 0 /dev/stdin | /usr/bin/sambamba sort -t $cores -m 8G -o \"$outdir/aligned.bam\" /dev/stdin\n" ; cwl:entryname "biscuit_align.sh" ] ] . a cwl:CommandLineTool ; rdfs:label "samtools index cram" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "cp" "$(inputs.cram.path)" "$(runtime.outdir)/$(inputs.cram.basename)" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "/opt/samtools/bin/samtools" "index" "$(runtime.outdir)/$(inputs.cram.basename)" "$(runtime.outdir)/$(inputs.cram.basename).crai" [ CommandLineBinding:shellQuote false ; cwl:valueFrom " && " ] "ln" "-s" "$(inputs.cram.basename).crai" "$(runtime.outdir)/$(inputs.cram.nameroot).crai" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:ShellCommandRequirement ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:ramMin 4000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/samtools-cwl:1.0.0" ] . cwl:source . sld:type xsd:int . a cwl:Workflow ; rdfs:label "Bisulfite alignment and QC" ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , , , , ; cwl:outputs , , , ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:source . cwl:source . sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "--min-read-length" ] ; sld:type xsd:int . cwl:inputBinding [ CommandLineBinding:position -2 ] ; sld:type xsd:string . a cwl:CommandLineTool ; rdfs:label "convert a biscuit pileup vcf to a bed and bedgraph file, via a wrapper script" ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( "$(runtime.outdir)/cpgs.bed.gz" "$(runtime.outdir)/cpgs.bedgraph" ) ; cwl:baseCommand ( "/bin/bash" "bsvcf2bed.sh" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs , ; cwl:requirements [ a cwl:InitialWorkDirRequirement ; cwl:listing [ cwl:entry "set -eou pipefail\n\npileup_vcf=\"$1\"\nreference=\"$2\"\ncpgs_bed_out=\"$3\"\ncpgs_bedgraph_out=\"$4\"\n\n#Creates a gzipped bed and a bedgraph that leaves out MT, random, GL contigs, etc\n/usr/bin/biscuit vcf2bed -t cg -k 1 -e \"$pileup_vcf\" | /usr/bin/biscuit mergecg \"$reference\" /dev/stdin -k 2 | tee >(/bin/gzip >\"$cpgs_bed_out\") | cut -f 1-4 | sort -k1,1 -k2,2n -S 12G | /usr/bin/perl -ne 'print $_ if $_ =~ /^(chr)?[1-9]?[0-9|X|Y]\\s/' >\"$cpgs_bedgraph_out\"\n" ; cwl:entryname "bsvcf2bed.sh" ] ] ; cwl:requirements [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 2 ; ResourceRequirement:ramMin 16000 ] ; cwl:requirements [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "mgibio/biscuit:0.3.8" ] . cwl:inputBinding [ CommandLineBinding:position -3 ] ; sld:type xsd:string . cwl:source . cwl:in , , , ; cwl:out ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "aligned.bam" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File .