@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: . @prefix CommandLineTool: . @prefix ExpressionTool: . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot + \"_aln_read_counts.txt\")" ] ; sld:type cwl:File . rdfs:comment "Applies deeptools plotFingerprint to generate meaningful plots for comparing IP and\ncontrol samples in terms of quality control. The main question which can be answered is:\nDid the antibody lead to enough enrichment that the IP can be distinguished from the control? \n" ; cwl:in , , , ; cwl:out , , ; cwl:run . rdfs:comment "qc files which shall be part of the multiqc summary;\noptional, only one of qc_files_array or qc_files_array_of_array \nmust be provided\n" ; sld:type sld:null ; sld:type [ sld:items cwl:File , sld:null ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . rdfs:comment "samtools sort - sorts unsorted bam file by coordinates." ; cwl:in ; cwl:out ; cwl:run . cwl:source . cwl:source . sld:type xsd:string . rdfs:comment "bam files to be merged" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.report_name + \"_report_data.zip\")" ] ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "*.sam" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*.sam" ] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "The effectively mappable genome size, please see: \nhttps://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html\n" ; sld:type xsd:long . rdfs:comment "number of reads aligned to the spike in genome, optional" ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--scaleFactor" ; cwl:valueFrom "${ \n if( self == null ){\n return null\n }\n else{\n return (1.0 / parseFloat(self)) \n }\n}\n" ] ; sld:type xsd:long , sld:null . sld:type xsd:string , sld:null . sld:type xsd:int , sld:null . cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "-2" ; cwl:valueFrom "${\n if ( inputs.is_paired_end ){\n return self;\n }\n else {\n return null;\n }\n} \n" ] ; cwl:inputBinding [ CommandLineBinding:position 12 ; CommandLineBinding:prefix "-2" ; cwl:valueFrom "${\n if ( inputs.is_paired_end ){\n return self;\n }\n else {\n return null;\n }\n} \n" ] ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 1 ; cwl:valueFrom "${\n if ( inputs.is_paired_end ){\n return null;\n }\n else {\n return \"--extendReads\";\n }\n}\n" ] [ CommandLineBinding:position 2 ; cwl:valueFrom "${\n if ( inputs.is_paired_end ){\n return null;\n }\n else {\n return inputs.fragment_size;\n }\n}\n" ] [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--labels" ; cwl:valueFrom "$(inputs.sample_id)" ] [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--plotFile" ; cwl:valueFrom "$(inputs.sample_id + \".plot_cov.png\")" ] [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--outRawCounts" ; cwl:valueFrom "$(inputs.sample_id + \".plot_cov.tsv\")" ] ) ; cwl:baseCommand ( "plotCoverage" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/deeptools:3.1.1" ] ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 15000 ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , , ; cwl:outputs , ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . rdfs:comment "name used for the html report and the corresponding zip file" ; cwl:default "multiqc" ; sld:type xsd:string . rdfs:comment "sorted bam input file" ; cwl:inputBinding [ CommandLineBinding:position 11 ; CommandLineBinding:prefix "INPUT=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . rdfs:comment "Adapter sequence for second reads - only for paired end data.\nif not specified, trim_galore will try to autodetect whether ...\n- Illumina universal adapter (AGATCGGAAGAGC)\n- Nextera adapter (CTGTCTCTTATA)\n- Illumina Small RNA 3' Adapter (TGGAATTCTCGG)\n... was used.\nYou can directly choose one of the above configurations\nby setting the adapter1 string to \"illumina\", \"nextera\", or \"small_rna\".\n" ; sld:type xsd:string , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . rdfs:comment "aligned reads to be checked in sam or bam format" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . cwl:in , , , , ; cwl:out , , ; cwl:run . cwl:source . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot)_filt.bam" ] ; sld:type cwl:File . rdfs:comment "trim galore - adapter trimming using trim_galore" ; cwl:in , , , ; cwl:out , , , , , , ; cwl:run . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File , sld:null . rdfs:comment "Bin size used for generation of coverage tracks. \nThe larger the bin size the smaller are the coverage tracks, however, \nthe less precise is the signal. For single bp resolution set to 1.\n" ; cwl:default 10 ; sld:type xsd:int . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$( inputs.sample_id + \".plot_fingerp.stderr\")" ] ; sld:type cwl:File . rdfs:comment "bowite2 - mapper, produces sam file" ; cwl:in , , , , ; cwl:out , ; cwl:run . cwl:outputSource ; sld:type [ sld:items [ sld:items cwl:File ; sld:type sld:array ] ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . rdfs:comment "html report of post-trimming fastqc" ; cwl:outputBinding [ CommandOutputBinding:glob "*fastqc.html" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Mean library fragment size, used to reconstruct entire \nfragments from single end reads. Not relevant in case of paired end data.\n" ; sld:type xsd:int , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; CommandLineTool:successCodes 1 , 0 , 2 ; cwl:arguments ( [ CommandLineBinding:position 1 ; cwl:valueFrom "${\n if ( inputs.is_paired_end ){\n return null;\n }\n else {\n return \"--extendReads\";\n }\n}\n" ] [ CommandLineBinding:position 2 ; cwl:valueFrom "${\n if ( inputs.is_paired_end ){\n return null;\n }\n else {\n return inputs.fragment_size;\n }\n}\n" ] [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--labels" ; cwl:valueFrom "$(inputs.sample_id)" ] [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--plotFile" ; cwl:valueFrom "$(inputs.sample_id + \".plot_fingerp.png\")" ] [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--outRawCounts" ; cwl:valueFrom "$(inputs.sample_id + \".plot_fingerp.tsv\")" ] ) ; cwl:baseCommand ( "plotFingerprint" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 15000 ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/deeptools:3.1.1" ] ; cwl:inputs , , , ; cwl:outputs , , ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "$( inputs.sample_id + \".plot_fingerp.stderr\")" . cwl:linkMerge "merge_flattened" ; cwl:source , , , , , , , , , . cwl:source . cwl:source . cwl:source . sld:type cwl:File , sld:null . cwl:source ; cwl:valueFrom "$(self + \"_spike_in.bam\")" . sld:type xsd:boolean . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source ; cwl:valueFrom "$(self + \".bam\")" . cwl:source . rdfs:comment "samtools sort - sorting of merged bam" ; cwl:in ; cwl:out ; cwl:run . sld:type xsd:boolean . cwl:outputSource ; sld:type cwl:File , sld:null . rdfs:comment "sorted bam input file" ; sld:type cwl:File . sld:type xsd:long , sld:null . cwl:source . cwl:secondaryFiles [] ; sld:type cwl:File . rdfs:comment "the effectively mappable genome size, \nsee: https://deeptools.readthedocs.io/en/latest/content/feature/effectiveGenomeSize.html\n" ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--effectiveGenomeSize" ] ; sld:type xsd:long . rdfs:comment "bam file as input; needs bai index file in the same directory" ; cwl:inputBinding [ CommandLineBinding:position 100 ; CommandLineBinding:prefix "--bam" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam_unsorted.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam_unsorted.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam_unsorted.basename)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam_unsorted.basename)" ] ; sld:type cwl:File . rdfs:comment "mean library fragment size; used to extend the reads" ; sld:type xsd:int , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "*unpaired_2.fq*" ] ; sld:type cwl:File , sld:null . rdfs:comment "samtools view - convert sam to bam" ; cwl:in ; cwl:out ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:outputSource ; sld:type [ sld:items [ sld:items cwl:File ; sld:type sld:array ] ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:outputSource ; sld:type cwl:File . cwl:source . sld:type xsd:int , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:position 1 ; cwl:valueFrom "-h" ] [ CommandLineBinding:position 1 ; cwl:valueFrom "-b" ] ) ; cwl:arguments ( [ CommandLineBinding:position 1 ; cwl:valueFrom "-h" ] [ CommandLineBinding:position 1 ; cwl:valueFrom "-b" ] ) ; cwl:baseCommand ( "samtools" "view" ) ; cwl:baseCommand ( "samtools" "view" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 10000 ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/samtools:1.7" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 10000 ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/samtools:1.7" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:stdout "$(inputs.sam.nameroot).bam" . cwl:source . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File , sld:null . rdfs:comment "fastqc - quality control for reads directly after mapping" ; cwl:in ; cwl:out , ; cwl:run . rdfs:comment "minimum overlap with adapter seq in bp needed to trim" ; cwl:default 1 ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--stringency" ] ; sld:type xsd:int . cwl:source . cwl:source . rdfs:comment "(optional) raw reads in fastq format; can be gzipped;\nif paired end, the file contains the second reads;\nif single end, the file does not exist\n" ; cwl:inputBinding [ CommandLineBinding:position 11 ] ; sld:type cwl:File , sld:null . rdfs:comment "discard reads that get shorter than this value" ; cwl:default 20 ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--length" ] ; sld:type xsd:int . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot + \".phantompeakqualtools_stdout\")" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "must be indexed" ; cwl:inputBinding [ CommandLineBinding:position 100 ; CommandLineBinding:prefix "--bamfiles" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--extendReads" ; cwl:valueFrom "${\n if ( inputs.is_paired_end ){\n return null;\n }\n else {\n return inputs.fragment_size;\n }\n}\n" ] [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--outFileName" ; cwl:valueFrom "$(inputs.bam.nameroot + \".bigwig\")" ] [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--outFileFormat" ; cwl:valueFrom "bigwig" ] [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--normalizeUsing" ; cwl:valueFrom "${ \n if( inputs.spike_in_count == null ){\n return \"RPGC\"\n }\n else{\n return null \n }\n}\n" ] ) ; cwl:baseCommand ( "bamCoverage" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 20000 ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/deeptools:3.1.1" ] ; cwl:inputs , , , , , , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . rdfs:comment "name of merged bam file" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type xsd:string . cwl:source . rdfs:comment "List of fastq files containing the second mate of raw reads in case of paired end \n(also see parameter \"fastq1\"). \nImportant: this list has to be of same length as parameter \"fastq1\" no matter if paired or single end is used. \nIn case of single end data specify \"null\" for every entry of fastq1. \n" ; sld:type [ sld:items cwl:File , sld:null ; sld:type sld:array ] . cwl:source . cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-c=" ; CommandLineBinding:separate false ] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . rdfs:comment "List of space-delimited chromosome names that shall be ignored \nwhen calculating the scaling factor. \nSpecify as space-delimited string. \nDefault: \"chrX chrY chrM\"\nSpecify as space-delimited string. \nDefault: \"chrX chrY chrM\"\n" ; cwl:default "chrX chrY chrM" ; sld:type xsd:string , sld:null . cwl:outputSource ; sld:type [ sld:items [ sld:items cwl:File ; sld:type sld:array ] ; sld:type sld:array ] . cwl:source . cwl:source . cwl:outputSource ; sld:type [ sld:items [ sld:items cwl:File ; sld:type sld:array ] ; sld:type sld:array ] . sld:type xsd:string . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "*unpaired_1.fq*" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.output_name)" ] ; sld:type cwl:File . rdfs:comment "aligned reads to be checked in sam or bam format" ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; cwl:inputBinding [ CommandLineBinding:position 2 ] ; sld:type cwl:File . sld:type xsd:int , sld:null . rdfs:comment "Adapter sequence for first reads. \nIf not specified (set to \"null\"), trim_galore will try to autodetect whether ...\\n\n- Illumina universal adapter (AGATCGGAAGAGC)\\n\n- Nextera adapter (CTGTCTCTTATA)\\n\n- Illumina Small RNA 3-prime Adapter (TGGAATTCTCGG)\\n\n... was used.\\n\nYou can directly choose one of the above configurations \nby setting the string to \"illumina\", \"nextera\", or \"small_rna\". \nOr you specify the adaptor string manually (e.g. \"AGATCGGAAGAGC\").\n" ; sld:type xsd:string , sld:null . rdfs:comment "if paired end, reads are extended" ; cwl:default true ; sld:type xsd:boolean . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; CommandLineTool:successCodes 2 , 1 , 0 ; cwl:arguments ( [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-tmpdir=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(runtime.tmpdir)" ] [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "-odir=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(runtime.outdir)" ] [ CommandLineBinding:position 100 ; CommandLineBinding:prefix "-savp=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(inputs.bam.nameroot + \".crosscor.pdf\")" ] [ CommandLineBinding:position 100 ; CommandLineBinding:prefix "-out=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(inputs.bam.nameroot + \".spp.out\")" ] ) ; cwl:baseCommand ( "Rscript" "--verbose" "--max-ppsize=500000" "/usr/bin/phantompeakqualtools-1.2/run_spp.R" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/phantompeakqualtools:1.2" ] ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 20000 ] ; cwl:inputs ; cwl:outputs , , , , ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "$(inputs.bam.nameroot + \".phantompeakqualtools_stderr\")" ; cwl:stdout "$(inputs.bam.nameroot + \".phantompeakqualtools_stdout\")" . cwl:source . cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputSource ; sld:type [ sld:items [ sld:items cwl:File ; sld:type sld:array ] ; sld:type sld:array ] . cwl:source . rdfs:comment "path to the FM-index files for the chosen genome genome" ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-x" ; cwl:valueFrom "$(self.path.replace(/\\.fa/i,\"\"))" ] ; cwl:inputBinding [ CommandLineBinding:position 2 ; CommandLineBinding:prefix "-x" ; cwl:valueFrom "$(self.path.replace(/\\.fa/i,\"\"))" ] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Sample ID used for naming the output files.\n" ; sld:type xsd:string . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "${\n var qc_files_array = inputs.qc_files_array;\n var qc_files_array_of_array = inputs.qc_files_array_of_array;\n var cmdline = \"echo 'copying input file ...'\";\n\n if ( qc_files_array != null ){\n for (var i=0; i ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/multiqc:1.7" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 10000 ] ; cwl:inputs , , ; cwl:outputs , ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:source . rdfs:comment "List of space-delimited chromosome names that shall be ignored \nwhen calculating the scaling factor. \nSpecify as space-delimited string. \nDefault: \"chrX chrY chrM\"\n" ; cwl:default "chrX chrY chrM" ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--ignoreForNormalization" ] ; sld:type xsd:string , sld:null . cwl:source . cwl:outputSource ; cwl:secondaryFiles [] ; sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:prefix "-o" ; cwl:valueFrom "$(runtime.outdir)" ] [ cwl:valueFrom "--noextract" ] ) ; cwl:arguments ( [ CommandLineBinding:prefix "-o" ; cwl:valueFrom "$(runtime.outdir)" ] [ cwl:valueFrom "--noextract" ] ) ; cwl:baseCommand ( "fastqc" ) ; cwl:baseCommand ( "fastqc" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 5000 ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/trim_galore:0.4.4_1.14_0.11.7" ] ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 5000 ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/trim_galore:0.4.4_1.14_0.11.7" ] ; cwl:inputs , , ; cwl:outputs , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:type xsd:boolean . cwl:inputBinding [ CommandLineBinding:position 11 ] ; cwl:inputBinding [ CommandLineBinding:position 11 ] ; sld:type cwl:File . cwl:source . rdfs:comment "If no user-defined fragment size was set,\nthe fragment size infered from cross-correlation analysis \nwill be used.\n" ; cwl:in , ; cwl:out ; cwl:run . rdfs:comment "html report showing results from zip" ; cwl:outputBinding [ CommandOutputBinding:glob "*_fastqc.html" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*_fastqc.html" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:baseCommand ( "samtools" "merge" ) ; cwl:baseCommand ( "samtools" "merge" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/samtools:1.7" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/samtools:1.7" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 20000 ] ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 20000 ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . cwl:in ; cwl:out , ; cwl:run . cwl:outputSource ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam_sorted.basename)" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "*trimming_report.txt" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "Adapter sequence for first reads.\nif not specified, trim_galore will try to autodetect whether ...\n- Illumina universal adapter (AGATCGGAAGAGC)\n- Nextera adapter (CTGTCTCTTATA)\n- Illumina Small RNA 3' Adapter (TGGAATTCTCGG)\n... was used.\nYou can directly choose one of the above configurations\nby setting the string to \"illumina\", \"nextera\", or \"small_rna\".\n" ; sld:type xsd:string , sld:null . cwl:source . rdfs:comment "if paired end, only properly paired reads pass" ; cwl:default true ; sld:type xsd:boolean . cwl:source . sld:type xsd:int , sld:null . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:source . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 2 ; cwl:valueFrom "MarkDuplicates" ] [ CommandLineBinding:position 13 ; CommandLineBinding:prefix "OUTPUT=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(inputs.bam_sorted.nameroot + \"_duprem.bam\")" ] [ CommandLineBinding:position 13 ; CommandLineBinding:prefix "METRICS_FILE=" ; CommandLineBinding:separate false ; cwl:valueFrom "$(inputs.bam_sorted.nameroot + \"_duprem.log\")" ] [ CommandLineBinding:position 14 ; cwl:valueFrom "REMOVE_DUPLICATES=TRUE" ] [ CommandLineBinding:position 15 ; cwl:valueFrom "ASSUME_SORTED=TRUE" ] [ CommandLineBinding:position 16 ; cwl:valueFrom "VALIDATION_STRINGENCY=SILENT" ] [ CommandLineBinding:position 17 ; cwl:valueFrom "VERBOSITY=INFO" ] [ CommandLineBinding:position 17 ; cwl:valueFrom "QUIET=false" ] ) ; cwl:baseCommand ( "java" "-jar" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/picard_tools:2.17.4" ] ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 20000 ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , ; cwl:outputs , ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "$(inputs.bam_sorted.nameroot + \".picard_markdup.log\")" . cwl:outputBinding [ CommandOutputBinding:glob "*val_2.fq*" ] ; sld:type cwl:File , sld:null . cwl:source . rdfs:comment "Path to reference genome in fasta format. \nBowtie2 index files (\".1.bt2\", \".2.bt2\", ...) as well as a samtools index (\".fai\") \nhas to be located in the same directory.\\n\nAll of these files can be downloaded for the most common genome builds at \nhttps://support.illumina.com/sequencing/sequencing_software/igenome.html. \nAlternatively, you can use \"bowtie2-build\" or \"samtools index\" to create them yourself.\n" ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_id + \".plot_fingerp.tsv\")" ] ; sld:type cwl:File , sld:null . cwl:source . cwl:source . rdfs:comment "deeptools plotCoverage - plots how many times a certain fraction of the \ngenome was covered (consideres the complete fragment between a reads pair).\n" ; cwl:in , , , ; cwl:out , ; cwl:run . rdfs:comment "samtools index - indexes sorted bam\n" ; cwl:in ; cwl:out ; cwl:run . cwl:outputSource ; sld:type cwl:File , sld:null . sld:type cwl:File . a cwl:Workflow ; 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:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] . cwl:source . rdfs:comment "samtools sort - sorting of filtered bam" ; cwl:in ; cwl:out ; cwl:run . sld:type xsd:int , sld:null . rdfs:comment "if only one read of a pair passes the qc and adapter trimming,\nit needs at least this length to be rescued\n" ; cwl:default 35 ; sld:type xsd:int . rdfs:comment "If paired end data is used set to true, else set to false.\n" ; cwl:default true ; sld:type xsd:boolean . rdfs:comment "Path to reference genome of the spike-in organism in fasta format. \nBowtie2 index files (\".1.bt2\", \".2.bt2\", ...) as well as a samtools index (\".fai\") \nhas to be located in the same directory.\\n\nAll of these files can be downloaded for the most common genome builds at \nhttps://support.illumina.com/sequencing/sequencing_software/igenome.html. \nAlternatively, you can use \"bowtie2-build\" or \"samtools index\" to create them yourself.\n" ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "*.spp.out" ; CommandOutputBinding:outputEval "$(parseInt(self[0].contents.split('\\t')[2]))" ; cwl:loadContents true ] ; sld:type xsd:int , sld:null . cwl:default 10 ; cwl:inputBinding [ CommandLineBinding:position 10 ; CommandLineBinding:prefix "--binSize" ] ; sld:type xsd:int . rdfs:comment "qc files which shall be part of the multiqc summary;\noptional, only one of qc_files_array or qc_files_array_of_array \nmust be provided\n" ; sld:type sld:null ; sld:type [ sld:items [ sld:items cwl:File , sld:null ; sld:type sld:array ] ; sld:type sld:array ] . sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "*.pdf" ] ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.report_name + \"_report.html\")" ] ; sld:type cwl:File . cwl:source . cwl:outputSource ; sld:type cwl:File , sld:null . rdfs:comment "multiqc summarizes the qc results from fastqc \nand other tools\n" ; cwl:in , , ; cwl:out , ; cwl:run . rdfs:comment "samtools view - convert sam to bam" ; cwl:in ; cwl:out ; cwl:run . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--fastqc_args" ; cwl:valueFrom "\"--noextract\"" ] [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--gzip" ] [ CommandLineBinding:position 1 ; cwl:valueFrom "${\n if ( inputs.adapter1 == \"illumina\" ){ return \"--illumina\" }\n else if ( inputs.adapter1 == \"nextera\" ){ return \"--nextera\" }\n else if ( inputs.adapter1 == \"small_rna\" ){ return \"--small_rna\" }\n else { return null }\n}\n" ] [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--adapter" ; cwl:valueFrom "${\n if ( inputs.apdater1 != null && inputs.adapter1 != \"illumina\" && inputs.adapter1 != \"nextera\" && inputs.adapter1 != \"small_rna\" ){\n return inputs.adapter1\n } else {\n return null\n }\n}\n" ] [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--adapter2" ; cwl:valueFrom "${\n if ( inputs.fastq2 != null && inputs.apdater2 != null && inputs.adapter1 != \"illumina\" && inputs.adapter1 != \"nextera\" && inputs.adapter1 != \"small_rna\" ){\n return inputs.adapter2\n } else {\n return null\n }\n}\n" ] [ CommandLineBinding:position 1 ; cwl:valueFrom "${\n if ( inputs.fastq2 == null ){ return null }\n else { return \"--paired\" }\n}\n" ] [ CommandLineBinding:position 1 ; cwl:valueFrom "${\n if ( inputs.fastq2 == null ){ return null }\n else { return \"--retain_unpaired\" }\n}\n" ] [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--length_1" ; cwl:valueFrom "${\n if ( inputs.fastq2 == null ){ return null }\n else { return inputs.min_unpaired_read_rescue_length }\n}\n" ] [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--length_2" ; cwl:valueFrom "${\n if ( inputs.fastq2 == null ){ return null }\n else { return inputs.min_unpaired_read_rescue_length }\n}\n" ] ) ; cwl:baseCommand ( "trim_galore" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 7000 ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/trim_galore:0.4.4_1.14_0.11.7" ] ; cwl:inputs , , , , , , , ; cwl:outputs , , , , , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . cwl:source . rdfs:comment "if false, reads are extended by fragment_size" ; sld:type xsd:boolean . rdfs:comment "samtools sort - sorts unsorted bam file by coordinates." ; cwl:in ; cwl:out ; cwl:run . sld:type xsd:string , sld:null . cwl:source . rdfs:comment "usefull for very long fragments, as expected for ATAC" ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--maxins" ] ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--maxins" ] ; sld:type xsd:long , sld:null . cwl:source . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File , sld:null . rdfs:comment "aligned reads to be checked in bam format" ; cwl:inputBinding [ CommandLineBinding:position 10 ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam_sorted.nameroot + \"_duprem.bam\")" ] ; sld:type cwl:File . cwl:source . rdfs:comment "bowite2 - mapper, produces sam file" ; cwl:in , , , ; cwl:out , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . sld:type xsd:int , sld:null . rdfs:comment "raw reads in fastq format; can be gzipped;\nif paired end, the file contains the first reads;\nif single end, the file contains all reads\n" ; cwl:inputBinding [ CommandLineBinding:position 10 ] ; sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ cwl:valueFrom "$(\"cp \" + inputs.bam_sorted.path + \" . && samtools index -b \" + inputs.bam_sorted.basename )" ] ) ; cwl:baseCommand ( "bash" "-c" ) ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 20000 ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/samtools:1.7" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . sld:type [ sld:items cwl:File , sld:null ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:inputBinding [ CommandLineBinding:position 1 ] ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:source . cwl:source . sld:type [ sld:items cwl:File ; sld:type sld:array ] . a cwl:ExpressionTool ; ns1:original_cwlVersion "v1.0" ; ExpressionTool:expression "${\n var fragment_size = inputs.user_def_fragment_size;\n if( fragment_size == null ){\n fragment_size = inputs.cc_fragment_size;\n }\n return { \"fragment_size\": fragment_size }\n}\n" ; cwl:cwlVersion ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 1000 ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . rdfs:comment "List of fastq files containing the first mate of raw reads. \nMuliple files are provided if multiplexing of the same library has been done \non multiple lanes. The reads comming from different fastq files are pooled \nafter alignment. Also see parameter \"fastq2\". \n" ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_id + \".plot_cov.tsv\")" ] ; sld:type cwl:File . cwl:in ; cwl:out , , , , ; cwl:run . cwl:outputSource ; sld:type cwl:File . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:position 1 ; cwl:valueFrom "--very-sensitive" ] [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-p" ; cwl:valueFrom "$(runtime.cores)" ] [ CommandLineBinding:position 10 ; cwl:valueFrom "${\n if ( inputs.is_paired_end ){\n return \"-1\";\n }\n else {\n return \"-U\";\n }\n}\n" ] [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-S" ; cwl:valueFrom "$(inputs.fastq1.nameroot + \".sam\")" ] ) ; cwl:arguments ( [ CommandLineBinding:position 1 ; cwl:valueFrom "--very-sensitive" ] [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-p" ; cwl:valueFrom "$(runtime.cores)" ] [ CommandLineBinding:position 10 ; cwl:valueFrom "${\n if ( inputs.is_paired_end ){\n return \"-1\";\n }\n else {\n return \"-U\";\n }\n}\n" ] [ CommandLineBinding:position 6 ; CommandLineBinding:prefix "-S" ; cwl:valueFrom "$(inputs.fastq1.nameroot + \".sam\")" ] ) ; cwl:baseCommand ( "bowtie2" ) ; cwl:baseCommand ( "bowtie2" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 30000 ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/bowtie2:2.2.6-2" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 30000 ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/bowtie2:2.2.6-2" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , ; cwl:outputs , ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stderr "$( inputs.fastq1.nameroot + \".bowtie2_stderr\")" . cwl:source . cwl:source . rdfs:comment "if paired end, only properly paired reads pass" ; cwl:default true ; sld:type xsd:boolean . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "*_aln_read_counts.txt" ; CommandOutputBinding:outputEval "$(parseInt(self[0].contents))" ; cwl:loadContents true ] ; sld:type xsd:long . cwl:source . rdfs:comment "samtools merge - merging bam files of lane replicates" ; cwl:in , ; cwl:out ; cwl:run . sld:type xsd:string . cwl:source . cwl:outputSource ; sld:type xsd:long . cwl:source . cwl:source . a cwl:CommandLineTool ; rdfs:comment "Sort a bam file by read names." ; ns1:original_cwlVersion "v1.2" ; cwl:arguments ( [ CommandLineBinding:prefix "-@" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:arguments ( [ CommandLineBinding:prefix "-@" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:arguments ( [ CommandLineBinding:prefix "-@" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:arguments ( [ CommandLineBinding:prefix "-@" ; cwl:valueFrom "$(runtime.cores)" ] ) ; cwl:baseCommand ( "samtools" "sort" ) ; cwl:baseCommand ( "samtools" "sort" ) ; cwl:baseCommand ( "samtools" "sort" ) ; cwl:baseCommand ( "samtools" "sort" ) ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 15000 ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/samtools:1.7" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 15000 ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 15000 ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/samtools:1.7" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/samtools:1.7" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/samtools:1.7" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 4 ; ResourceRequirement:ramMin 15000 ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs ; cwl:outputs ; cwl:stdout "$(inputs.bam_unsorted.basename)" . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , ; cwl:cwlVersion ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:inputs , , , , , , ; cwl:outputs , , , , , , , , ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 1 ; cwl:valueFrom "-c" ] [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-F" ; cwl:valueFrom "4" ] [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-q" ; cwl:valueFrom "20" ] [ CommandLineBinding:position 2 ; cwl:valueFrom "${\n if ( inputs.is_paired_end ){\n return \"-f\";\n }\n else {\n return null;\n }\n}\n" ] [ CommandLineBinding:position 3 ; cwl:valueFrom "${\n if ( inputs.is_paired_end ){\n return \"3\";\n }\n else {\n return null;\n }\n}\n" ] ) ; cwl:baseCommand ( "samtools" "view" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 10000 ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/samtools:1.7" ] ; cwl:inputs , ; cwl:outputs , ; cwl:stdout "$(inputs.bam.nameroot + \"_aln_read_counts.txt\")" . cwl:outputBinding [ CommandOutputBinding:glob "$( inputs.fastq1.nameroot + \".bowtie2_stderr\")" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$( inputs.fastq1.nameroot + \".bowtie2_stderr\")" ] ; sld:type cwl:File . sld:type xsd:string . sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:source . sld:type xsd:boolean . rdfs:comment "samtools merge - merging bam files of lane replicates" ; cwl:in , ; cwl:out ; cwl:run . cwl:linkMerge "merge_flattened" ; cwl:source , , , , . a cwl:Workflow ; 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:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . rdfs:comment "trim all base with a phred score lower than this valueFrom" ; cwl:default 20 ; cwl:inputBinding [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "--quality" ] ; sld:type xsd:int . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_id + \".plot_cov.png\")" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "*.spp.out" ] ; sld:type cwl:File , sld:null . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam_sorted.nameroot + \".picard_markdup.log\")" ] ; sld:type cwl:File . cwl:in , , , , , ; cwl:out , , , , , , , , ; cwl:run ; cwl:scatter ( ) ; cwl:scatterMethod ScatterMethod:dotproduct . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:in , , , , , , ; cwl:out ; cwl:run . a cwl:Workflow ; 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:requirements [ a cwl:ScatterFeatureRequirement ] ; cwl:requirements [ a cwl:MultipleInputFeatureRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] . cwl:in , , ; cwl:out , , ; cwl:run . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sample_id + \".plot_fingerp.png\")" ] ; sld:type cwl:File , sld:null . a cwl:CommandLineTool ; ns1:original_cwlVersion "v1.0" ; cwl:arguments ( [ CommandLineBinding:position 1 ; cwl:valueFrom "-h" ] [ CommandLineBinding:position 1 ; cwl:valueFrom "-b" ] [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-F" ; cwl:valueFrom "4" ] [ CommandLineBinding:position 1 ; CommandLineBinding:prefix "-q" ; cwl:valueFrom "20" ] [ CommandLineBinding:position 2 ; cwl:valueFrom "${\n if ( inputs.is_paired_end ){\n return \"-f\";\n }\n else {\n return null;\n }\n}\n" ] [ CommandLineBinding:position 3 ; cwl:valueFrom "${\n if ( inputs.is_paired_end ){\n return \"3\";\n }\n else {\n return null;\n }\n}\n" ] ) ; cwl:baseCommand ( "samtools" "view" ) ; cwl:cwlVersion ; cwl:hints [ a cwl:ResourceRequirement ; ResourceRequirement:coresMin 1 ; ResourceRequirement:ramMin 10000 ] ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:hints [ a cwl:DockerRequirement ; DockerRequirement:dockerPull "kerstenbreuer/samtools:1.7" ] ; cwl:inputs , ; cwl:outputs ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:stdout "$(inputs.bam.nameroot)_filt.bam" . cwl:default "/bin/picard.jar" ; cwl:inputBinding [ CommandLineBinding:position 1 ] ; sld:type xsd:string . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sam.nameroot).bam" ] ; cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.sam.nameroot).bam" ] ; sld:type cwl:File . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot + \".bigwig\")" ] ; sld:type cwl:File . a cwl:Workflow ; ns1:original_cwlVersion "v1.0" ; Workflow:steps , , , , , ; cwl:cwlVersion ; cwl:hints [ a ; NetworkAccess:networkAccess true ] ; cwl:hints [ a ; LoadListingRequirement:loadListing "deep_listing" ] ; cwl:inputs , , ; cwl:outputs , , ; cwl:requirements [ a cwl:InlineJavascriptRequirement ] ; cwl:requirements [ a cwl:StepInputExpressionRequirement ] ; cwl:requirements [ a cwl:SubworkflowFeatureRequirement ] ; cwl:requirements [ a cwl:ScatterFeatureRequirement ] . sld:type xsd:boolean . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . rdfs:comment "must be indexed" ; cwl:inputBinding [ CommandLineBinding:position 100 ; CommandLineBinding:prefix "--bamfiles" ] ; cwl:secondaryFiles [] ; sld:type cwl:File . cwl:in , , , ; cwl:out , , , , , , , , , ; cwl:run . rdfs:comment "samtools view" ; cwl:in , ; cwl:out ; cwl:run . cwl:source . rdfs:comment "remove duplicate reads" ; cwl:in ; cwl:out ; cwl:run . rdfs:comment "aligned reads to be checked in bam format" ; cwl:inputBinding [ CommandLineBinding:position 10 ] ; sld:type cwl:File . cwl:outputSource ; sld:type xsd:int , sld:null . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "$(inputs.bam.nameroot + \".phantompeakqualtools_stderr\")" ] ; sld:type cwl:File . rdfs:comment "if paired end, reads are extended" ; cwl:default true ; sld:type xsd:boolean . cwl:outputSource ; sld:type cwl:File . rdfs:comment "Adapter sequence for second reads (only relevant for paired end data). \nIf it is not specified (set to \"null\"), trim_galore will try to autodetect whether ...\\n\n- Illumina universal adapter (AGATCGGAAGAGC)\\n\n- Nextera adapter (CTGTCTCTTATA)\\n\n- Illumina Small RNA 3-prime Adapter (TGGAATTCTCGG)\\n\n... was used.\\n\nYou can directly choose one of the above configurations \nby setting the string to \"illumina\", \"nextera\", or \"small_rna\". \nOr you specify the adaptor string manually (e.g. \"AGATCGGAAGAGC\").\n" ; sld:type xsd:string , sld:null . rdfs:comment "fastqc - quality control for trimmed fastq" ; cwl:in , ; cwl:out , ; cwl:run . rdfs:comment "all data of post-trimming fastqc e.g. figures" ; cwl:outputBinding [ CommandOutputBinding:glob "*fastqc.zip" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:source . cwl:outputBinding [ CommandOutputBinding:glob "${\n if ( inputs.fastq2 == null ){ return \"*trimmed.fq*\" }\n else { return \"*val_1.fq*\" }\n}\n" ] ; sld:type cwl:File . cwl:source . rdfs:comment "all data e.g. figures" ; cwl:outputBinding [ CommandOutputBinding:glob "*_fastqc.zip" ] ; cwl:outputBinding [ CommandOutputBinding:glob "*_fastqc.zip" ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] ; sld:type [ sld:items cwl:File ; sld:type sld:array ] . cwl:outputSource ; sld:type cwl:File . cwl:outputSource ; sld:type cwl:File , sld:null . cwl:outputSource ; sld:type cwl:File .