@prefix LoadListingRequirement: <http://commonwl.org/cwltool#LoadListingRequirement/> .
@prefix CommandLineBinding: <https://w3id.org/cwl/cwl#CommandLineBinding/> .
@prefix xsd:   <http://www.w3.org/2001/XMLSchema#> .
@prefix DockerRequirement: <https://w3id.org/cwl/cwl#DockerRequirement/> .
@prefix Workflow: <https://w3id.org/cwl/cwl#Workflow/> .
@prefix sld:   <https://w3id.org/cwl/salad#> .
@prefix rdfs:  <http://www.w3.org/2000/01/rdf-schema#> .
@prefix CommandOutputBinding: <https://w3id.org/cwl/cwl#CommandOutputBinding/> .
@prefix ns1:   <http://commonwl.org/cwltool#> .
@prefix NetworkAccess: <http://commonwl.org/cwltool#NetworkAccess/> .
@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix ScatterMethod: <https://w3id.org/cwl/cwl#ScatterMethod/> .
@prefix cwl:   <https://w3id.org/cwl/cwl#> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#output_fastqc_data_files_read1>
        rdfs:comment      "FastQC data files for paired read 1" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read1/output_fastqc_data_file> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_fastqc_reads_read2>
        cwl:in             <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_fastqc_reads_read2/input_basename> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_fastqc_reads_read2/input_fastqc_data> ;
        cwl:out            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_fastqc_reads_read2/output_fastqc_read_count> ;
        cwl:run            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/count-fastqc-reads.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_fastqc_reads_read2/input_fastqc_data> <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_fastqc_reads_read2/input_basename> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl>
        a                        cwl:Workflow ;
        rdfs:comment             "ChIP-seq 01 QC - reads: PE" ;
        ns1:original_cwlVersion  "v1.0" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_basename_read2> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#compare_read_counts_read2> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read1> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#fastqc_read2> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_fastqc_reads_read1> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_basename_read1> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_fastqc_reads_read2> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read2> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read2> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#fastqc_read1> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read2> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#compare_read_counts_read1> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read1> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read1> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#default_adapters_file> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#input_read1_fastq_files> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#nthreads> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#input_read2_fastq_files> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#output_fastqc_data_files_read1> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#output_count_raw_reads_read1> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#output_diff_counts_read2> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#output_diff_counts_read1> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#output_count_raw_reads_read2> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#output_custom_adapters_read1> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#output_fastqc_report_files_read1> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#output_fastqc_report_files_read2> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#output_fastqc_data_files_read2> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#output_custom_adapters_read2> ;
        cwl:requirements         [ a  cwl:ScatterFeatureRequirement ] ;
        cwl:requirements         [ a  cwl:StepInputExpressionRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read2/input_basename>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_basename_read2/output_basename> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#input_read1_fastq_files>
        rdfs:comment  "Input read1 fastq files" ;
        sld:type      [ sld:items  cwl:File ;
                        sld:type   sld:array
                      ] .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_basename_read1>
        cwl:in       <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_basename_read1/input_file> ;
        cwl:out      <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_basename_read1/output_basename> ;
        cwl:run      <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/extract-basename.cwl> ;
        cwl:scatter  ( <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_basename_read1/input_file> ) .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/overrepresented_sequence_extract.cwl#default_adapters_file>
        rdfs:comment      "Adapters file in fasta format" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/overrepresented_sequence_extract.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.input_basename + '.custom_adapters.fasta')"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  3 ;
                                     cwl:valueFrom                "$(inputs.input_basename + '.custom_adapters.fasta')"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "overrepresented_sequence_extract.py" ) ;
        cwl:baseCommand          ( "overrepresented_sequence_extract.py" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/v1.2> ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "reddylab/overrepresented_sequence_extract:1.0"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "reddylab/overrepresented_sequence_extract:1.0"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/overrepresented_sequence_extract.cwl#input_basename> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/overrepresented_sequence_extract.cwl#default_adapters_file> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/overrepresented_sequence_extract.cwl#input_fastqc_data> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/overrepresented_sequence_extract.cwl#output_custom_adapters> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/diff.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:comment             "Compares 2 files" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "diff" ) ;
        cwl:baseCommand          ( "diff" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "reddylab/workflow-utils:ggr"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "reddylab/workflow-utils:ggr"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/diff.cwl#file1> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/diff.cwl#brief> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/diff.cwl#file2> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/diff.cwl#result> ;
        cwl:stdout               "stdout.txt" .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#output_count_raw_reads_read1>
        cwl:outputSource  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read1/output_read_count> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read1/input_basename>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_basename_read1/output_basename> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read2>
        cwl:in             <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read2/input_fastq_file> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read2/input_basename> ;
        cwl:out            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read2/output_read_count> ;
        cwl:run            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/count-fastq-reads.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read2/input_fastq_file> <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read2/input_basename> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/count-fastqc-reads.cwl#output_fastqc_read_count>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.input_basename + '.fastqc-read_count.txt')" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.input_basename + '.fastqc-read_count.txt')" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/extract_fastqc_data.cwl#pipe>
        cwl:default       true ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-p"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-p"
                          ] ;
        sld:type          xsd:boolean .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/count-fastqc-reads.cwl#input_fastqc_data>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_fastqc_reads_read1/input_basename>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_basename_read1/output_basename> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/extract-basename.cwl#input_file>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#output_diff_counts_read2>
        cwl:outputSource  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#compare_read_counts_read2/result> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/fastqc.cwl#output_qc_report_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.input_fastq_file.path.replace(/^.*[\\\\\\/]/, \"\").replace(/\\.[^/.]+$/, '') + \"_fastqc.zip\")" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.input_fastq_file.path.replace(/^.*[\\\\\\/]/, \"\").replace(/\\.[^/.]+$/, '') + \"_fastqc.zip\")" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#compare_read_counts_read1/file2>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_fastqc_reads_read1/output_fastqc_read_count> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read2/input_qc_report_file>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#fastqc_read2/output_qc_report_file> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/count-fastqc-reads.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:comment             "Extracts read count from fastqc_data.txt" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "count-fastqc_data-reads.sh" ) ;
        cwl:baseCommand          ( "count-fastqc_data-reads.sh" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/v1.2> ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "reddylab/workflow-utils:ggr"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "reddylab/workflow-utils:ggr"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/count-fastqc-reads.cwl#input_fastqc_data> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/count-fastqc-reads.cwl#input_basename> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/count-fastqc-reads.cwl#output_fastqc_read_count> ;
        cwl:stdout               "$(inputs.input_basename + '.fastqc-read_count.txt')" .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read2/input_basename>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_basename_read2/output_basename> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#output_fastqc_report_files_read2>
        rdfs:comment      "FastQC reports in zip format for paired read 1" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#fastqc_read2/output_qc_report_file> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_fastqc_reads_read1/input_fastqc_data>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read1/output_fastqc_data_file> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/overrepresented_sequence_extract.cwl#output_custom_adapters>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.input_basename + '.custom_adapters.fasta')" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.input_basename + '.custom_adapters.fasta')" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read2>
        cwl:in             <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read2/input_basename> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read2/input_qc_report_file> ;
        cwl:out            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read2/output_fastqc_data_file> ;
        cwl:run            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/extract_fastqc_data.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read2/input_qc_report_file> <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read2/input_basename> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#output_custom_adapters_read2>
        cwl:outputSource  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read2/output_custom_adapters> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/extract_fastqc_data.cwl#output_fastqc_data_file>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.input_basename + '.fastqc_data.txt')" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.input_basename + '.fastqc_data.txt')" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#fastqc_read2>
        cwl:in       <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#fastqc_read2/input_fastq_file> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#fastqc_read2/threads> ;
        cwl:out      <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#fastqc_read2/output_qc_report_file> ;
        cwl:run      <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/fastqc.cwl> ;
        cwl:scatter  ( <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#fastqc_read2/input_fastq_file> ) .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#default_adapters_file>
        rdfs:comment  "Adapters file" ;
        sld:type      cwl:File .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/fastqc.cwl#input_fastq_file>
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          4 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read2/input_fastq_file>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#input_read2_fastq_files> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/diff.cwl#file1>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_fastqc_reads_read2/input_fastqc_data>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read2/output_fastqc_data_file> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read2/input_basename>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_basename_read2/output_basename> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#fastqc_read2/threads>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#nthreads> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read2/default_adapters_file>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#default_adapters_file> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/count-fastq-reads.cwl#output_read_count>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.input_basename + '.read_count.txt')" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "$(inputs.input_basename + '.read_count.txt')" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read1>
        cwl:in             <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read1/default_adapters_file> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read1/input_fastqc_data> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read1/input_basename> ;
        cwl:out            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read1/output_custom_adapters> ;
        cwl:run            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/overrepresented_sequence_extract.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read1/input_fastqc_data> <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read1/input_basename> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read1/input_basename>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_basename_read1/output_basename> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#nthreads>
        rdfs:comment  "Number of threads." ;
        sld:type      xsd:int .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/overrepresented_sequence_extract.cwl#input_basename>
        rdfs:comment  "Name of the sample - used as a base name for generating output files" ;
        sld:type      xsd:string .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/overrepresented_sequence_extract.cwl#input_fastqc_data>
        rdfs:comment      "fastqc_data.txt file from a fastqc report" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read1/input_fastq_file>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#input_read1_fastq_files> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#output_fastqc_data_files_read2>
        rdfs:comment      "FastQC data files for paired read 1" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read2/output_fastqc_data_file> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_basename_read2>
        cwl:in       <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_basename_read2/input_file> ;
        cwl:out      <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_basename_read2/output_basename> ;
        cwl:run      <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/extract-basename.cwl> ;
        cwl:scatter  ( <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_basename_read2/input_file> ) .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#output_count_raw_reads_read2>
        cwl:outputSource  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read2/output_read_count> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/count-fastq-reads.cwl#input_basename>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/fastqc.cwl#threads>
        cwl:default       1 ;
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            CommandLineBinding:prefix    "--threads"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  5 ;
                            CommandLineBinding:prefix    "--threads"
                          ] ;
        sld:type          xsd:int .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/extract_fastqc_data.cwl#input_basename>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_basename_read1/input_file>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#input_read1_fastq_files> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#compare_read_counts_read1>
        cwl:in             <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#compare_read_counts_read1/file1> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#compare_read_counts_read1/file2> ;
        cwl:out            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#compare_read_counts_read1/result> ;
        cwl:run            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/diff.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#compare_read_counts_read1/file1> <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#compare_read_counts_read1/file2> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#compare_read_counts_read2/file1>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read2/output_read_count> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/fastqc.cwl#noextract>
        cwl:default       true ;
        cwl:inputBinding  [ CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "--noextract"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  2 ;
                            CommandLineBinding:prefix    "--noextract"
                          ] ;
        sld:type          xsd:boolean .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/diff.cwl#brief>
        cwl:default       true ;
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "--brief"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "--brief"
                          ] ;
        sld:type          xsd:boolean .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/extract_fastqc_data.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:comment             "Unzips a zipped fastqc report and returns the fastqc_data.txt file. Unzips the file to pipe and uses redirection" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "unzip" ) ;
        cwl:baseCommand          ( "unzip" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "dukegcb/fastqc"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "dukegcb/fastqc"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/extract_fastqc_data.cwl#extract_pattern> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/extract_fastqc_data.cwl#input_qc_report_file> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/extract_fastqc_data.cwl#pipe> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/extract_fastqc_data.cwl#input_basename> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/extract_fastqc_data.cwl#output_fastqc_data_file> ;
        cwl:stdout               "$(inputs.input_basename + '.fastqc_data.txt')" .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read1/input_basename>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_basename_read1/output_basename> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/extract-basename.cwl#output_basename>
        cwl:outputBinding  [ CommandOutputBinding:outputEval
                          "$(inputs.input_file.path.substr(inputs.input_file.path.lastIndexOf('/') + 1, inputs.input_file.path.lastIndexOf('.') - (inputs.input_file.path.lastIndexOf('/') + 1)))" ] ;
        cwl:outputBinding  [ CommandOutputBinding:outputEval
                          "$(inputs.input_file.path.substr(inputs.input_file.path.lastIndexOf('/') + 1, inputs.input_file.path.lastIndexOf('.') - (inputs.input_file.path.lastIndexOf('/') + 1)))" ] ;
        sld:type           xsd:string .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_fastqc_reads_read1>
        cwl:in             <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_fastqc_reads_read1/input_fastqc_data> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_fastqc_reads_read1/input_basename> ;
        cwl:out            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_fastqc_reads_read1/output_fastqc_read_count> ;
        cwl:run            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/count-fastqc-reads.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_fastqc_reads_read1/input_fastqc_data> <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_fastqc_reads_read1/input_basename> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/diff.cwl#file2>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/extract_fastqc_data.cwl#extract_pattern>
        cwl:default       "*/fastqc_data.txt" ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          3 ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/fastqc.cwl>
        a                        cwl:CommandLineTool ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:arguments            ( [ CommandLineBinding:position  5 ;
                                     CommandLineBinding:prefix    "--dir" ;
                                     cwl:valueFrom                "$(runtime.tmpdir)"
                                   ]
                                   [ CommandLineBinding:position  5 ;
                                     CommandLineBinding:prefix    "-o" ;
                                     cwl:valueFrom                "$(runtime.outdir)"
                                   ]
                                 ) ;
        cwl:arguments            ( [ CommandLineBinding:position  5 ;
                                     CommandLineBinding:prefix    "--dir" ;
                                     cwl:valueFrom                "$(runtime.tmpdir)"
                                   ]
                                   [ CommandLineBinding:position  5 ;
                                     CommandLineBinding:prefix    "-o" ;
                                     cwl:valueFrom                "$(runtime.outdir)"
                                   ]
                                 ) ;
        cwl:baseCommand          ( "fastqc" ) ;
        cwl:baseCommand          ( "fastqc" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/v1.2> ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "dukegcb/fastqc"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "dukegcb/fastqc"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/fastqc.cwl#format> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/fastqc.cwl#threads> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/fastqc.cwl#noextract> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/fastqc.cwl#input_fastq_file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/fastqc.cwl#output_qc_report_file> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/count-fastqc-reads.cwl#input_basename>
        sld:type  xsd:string .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_basename_read2/input_file>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#input_read2_fastq_files> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read1>
        cwl:in             <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read1/input_fastq_file> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read1/input_basename> ;
        cwl:out            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read1/output_read_count> ;
        cwl:run            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/count-fastq-reads.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read1/input_fastq_file> <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read1/input_basename> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read2>
        cwl:in             <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read2/input_fastqc_data> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read2/default_adapters_file> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read2/input_basename> ;
        cwl:out            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read2/output_custom_adapters> ;
        cwl:run            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/overrepresented_sequence_extract.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read2/input_fastqc_data> <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read2/input_basename> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/extract_fastqc_data.cwl#input_qc_report_file>
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          2 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read1/input_fastqc_data>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read1/output_fastqc_data_file> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#input_read2_fastq_files>
        rdfs:comment  "Input read2 fastq files" ;
        sld:type      [ sld:items  cwl:File ;
                        sld:type   sld:array
                      ] .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#fastqc_read2/input_fastq_file>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#input_read2_fastq_files> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#output_diff_counts_read1>
        cwl:outputSource  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#compare_read_counts_read1/result> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/fastqc.cwl#format>
        cwl:default       "fastq" ;
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "--format"
                          ] ;
        cwl:inputBinding  [ CommandLineBinding:position  3 ;
                            CommandLineBinding:prefix    "--format"
                          ] ;
        sld:type          xsd:string .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/diff.cwl#result>
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "stdout.txt" ] ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "stdout.txt" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#compare_read_counts_read1/file1>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_raw_reads_read1/output_read_count> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/count-fastq-reads.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:comment             "Counts reads in a fastq file" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "count-fastq-reads.sh" ) ;
        cwl:baseCommand          ( "count-fastq-reads.sh" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/v1.2> ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "reddylab/workflow-utils:ggr"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "reddylab/workflow-utils:ggr"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/count-fastq-reads.cwl#input_basename> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/count-fastq-reads.cwl#input_fastq_file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/count-fastq-reads.cwl#output_read_count> ;
        cwl:stdout               "$(inputs.input_basename + '.read_count.txt')" .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/extract-basename.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:comment             "Extracts the base name of a file" ;
        ns1:original_cwlVersion  "v1.2" ;
        cwl:baseCommand          ( "echo" ) ;
        cwl:baseCommand          ( "echo" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/v1.2> ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "reddylab/workflow-utils:ggr"
                                 ] ;
        cwl:hints                [ a                            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/NetworkAccess> ;
                                   NetworkAccess:networkAccess  true
                                 ] ;
        cwl:hints                [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "reddylab/workflow-utils:ggr"
                                 ] ;
        cwl:hints                [ a       <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/LoadListingRequirement> ;
                                   LoadListingRequirement:loadListing
                                           "deep_listing"
                                 ] ;
        cwl:inputs               <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/extract-basename.cwl#input_file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/extract-basename.cwl#output_basename> ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] ;
        cwl:requirements         [ a  cwl:InlineJavascriptRequirement ] .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#output_fastqc_report_files_read1>
        rdfs:comment      "FastQC reports in zip format for paired read 1" ;
        cwl:outputSource  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#fastqc_read1/output_qc_report_file> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#output_custom_adapters_read1>
        cwl:outputSource  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read1/output_custom_adapters> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read1>
        cwl:in             <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read1/input_qc_report_file> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read1/input_basename> ;
        cwl:out            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read1/output_fastqc_data_file> ;
        cwl:run            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/extract_fastqc_data.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read1/input_qc_report_file> <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read1/input_basename> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_fastqc_reads_read2/input_basename>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_basename_read2/output_basename> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read2/input_fastqc_data>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read2/output_fastqc_data_file> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#fastqc_read1>
        cwl:in       <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#fastqc_read1/input_fastq_file> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#fastqc_read1/threads> ;
        cwl:out      <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#fastqc_read1/output_qc_report_file> ;
        cwl:run      <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/fastqc.cwl> ;
        cwl:scatter  ( <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#fastqc_read1/input_fastq_file> ) .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#extract_fastqc_data_read1/input_qc_report_file>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#fastqc_read1/output_qc_report_file> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#fastqc_read1/input_fastq_file>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#input_read1_fastq_files> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/utils/count-fastq-reads.cwl#input_fastq_file>
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        cwl:inputBinding  [ CommandLineBinding:position
                          1 ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#fastqc_read1/threads>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#nthreads> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#compare_read_counts_read2>
        cwl:in             <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#compare_read_counts_read2/file2> , <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#compare_read_counts_read2/file1> ;
        cwl:out            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#compare_read_counts_read2/result> ;
        cwl:run            <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/qc/diff.cwl> ;
        cwl:scatter        ( <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#compare_read_counts_read2/file1> <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#compare_read_counts_read2/file2> ) ;
        cwl:scatterMethod  ScatterMethod:dotproduct .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#compare_read_counts_read2/file2>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#count_fastqc_reads_read2/output_fastqc_read_count> .

<https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#overrepresented_sequence_extract_read1/default_adapters_file>
        cwl:source  <https://w3id.org/cwl/view/git/c50b80e9b0eaaf4613f9feca44b3463bbfd288d5/v1.0/ChIP-seq_pipeline/01-qc-pe.cwl#default_adapters_file> .