@prefix rdf:   <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@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 cwl:   <https://w3id.org/cwl/cwl#> .
@prefix Workflow: <https://w3id.org/cwl/cwl#Workflow/> .
@prefix ResourceRequirement: <https://w3id.org/cwl/cwl#ResourceRequirement/> .
@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#> .

<https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/call_peaks.cwl#call_peaks.cwl>
        a                        cwl:CommandLineTool ;
        rdfs:label               "call peaks" ;
        ns1:original_cwlVersion  "v1.1" ;
        cwl:baseCommand          ( "macs2" "callpeak" ) ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/v1.2> ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/call_peaks.cwl#call_peaks.cwl/bam_file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/call_peaks.cwl#call_peaks.cwl/r_script> , <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/call_peaks.cwl#call_peaks.cwl/bed_graphs> , <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/call_peaks.cwl#call_peaks.cwl/narrow_peaks> , <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/call_peaks.cwl#call_peaks.cwl/peaks_table> , <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/call_peaks.cwl#call_peaks.cwl/summits_bed> ;
        cwl:requirements         [ a                             cwl:DockerRequirement ;
                                   DockerRequirement:dockerPull  "hubmap/sc-atac-seq-hg38:2.2.4"
                                 ] ;
        cwl:requirements         [ a                              cwl:ResourceRequirement ;
                                   ResourceRequirement:coresMin   1 ;
                                   ResourceRequirement:outdirMin  100000 ;
                                   ResourceRequirement:ramMin     1024
                                 ] .

<https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#narrow_peaks>
        cwl:outputSource  <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#call_peaks/narrow_peaks> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#bam_file>
        sld:type  cwl:File .

<https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/call_peaks.cwl#call_peaks.cwl/peaks_table>
        rdfs:comment       "Tabular file containing peak data" ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.xls" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#call_peaks/bam_file>
        cwl:source  <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#bam_file> .

<https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/call_peaks.cwl#call_peaks.cwl/bam_file>
        rdfs:comment      "The bam file to call peaks on" ;
        cwl:inputBinding  [ CommandLineBinding:position  1 ;
                            CommandLineBinding:prefix    "-t"
                          ] ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/call_peaks.cwl#call_peaks.cwl/summits_bed>
        rdfs:comment       "BED file containing summit locations for every peak" ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.bed" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#summits_bed>
        cwl:outputSource  <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#call_peaks/summits_bed> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#call_peaks>
        cwl:in   <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#call_peaks/bam_file> ;
        cwl:out  <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#call_peaks/bed_graphs> , <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#call_peaks/peaks_table> , <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#call_peaks/r_script> , <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#call_peaks/summits_bed> , <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#call_peaks/narrow_peaks> ;
        cwl:run  <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/call_peaks.cwl> .

<https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl>
        a                        cwl:Workflow ;
        ns1:original_cwlVersion  "v1.1" ;
        Workflow:steps           <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#call_peaks> ;
        cwl:cwlVersion           <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/v1.2> ;
        cwl:inputs               <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#bam_file> ;
        cwl:outputs              <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#r_script> , <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#summits_bed> , <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#bed_graphs> , <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#peaks_table> , <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#narrow_peaks> .

<https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#bed_graphs>
        cwl:outputSource  <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#call_peaks/bed_graphs> ;
        sld:type          [ sld:items  cwl:File ;
                            sld:type   sld:array
                          ] .

<https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/call_peaks.cwl#call_peaks.cwl/bed_graphs>
        rdfs:comment       "Bed graph files containing information about pileup signals and local biases" ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.bdg" ] ;
        sld:type           [ sld:items  cwl:File ;
                             sld:type   sld:array
                           ] .

<https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/call_peaks.cwl#call_peaks.cwl/narrow_peaks>
        rdfs:comment       "BED6+4 format file which contains the peak locations together with peak summit, p-value, and q-value. Can be loaded into UCSC genome browser" ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.narrowPeak" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#r_script>
        cwl:outputSource  <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#call_peaks/r_script> ;
        sld:type          cwl:File .

<https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/call_peaks.cwl#call_peaks.cwl/r_script>
        rdfs:comment       "An r script for generating a pdf of model based on data" ;
        cwl:outputBinding  [ CommandOutputBinding:glob
                          "*.r" ] ;
        sld:type           cwl:File .

<https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#peaks_table>
        cwl:outputSource  <https://w3id.org/cwl/view/git/ec8a7e87c40f0c98cb649d4ffa1fc52e44fffb27/sc-atac-seq-pipeline/steps/bulk_analysis.cwl#call_peaks/peaks_table> ;
        sld:type          cwl:File .