{"@id":"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/DNase-seq_pipeline/pipeline-se.cwl","retrievedFrom":{"repoUrl":"https://github.com/alexbarrera/GGR-cwl.git","branch":"81555a89cc2d16bd3ab131a6685a44b44f08f927","path":"v1.0/DNase-seq_pipeline/pipeline-se.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/alexbarrera/GGR-cwl/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/DNase-seq_pipeline/pipeline-se.cwl","url":"https://github.com/alexbarrera/GGR-cwl/blob/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/DNase-seq_pipeline/pipeline-se.cwl"},"retrievedOn":"2026-10-15T16:26:53.123+00:00","lastCommit":"81555a89cc2d16bd3ab131a6685a44b44f08f927","label":"pipeline-se.cwl","doc":"DNase-seq pipeline - reads: SE","inputs":{"nthreads_map":{"doc":"Number of threads required for the 03-map step","type":"Integer"},"nthreads_quant":{"doc":"Number of threads required for the 05-quantification step","type":"Integer"},"genome_sizes_file":{"doc":"Genome sizes tab-delimited file (used in samtools)","type":"File"},"input_fastq_files":{"type":"File[]"},"nthreads_peakcall":{"doc":"Number of threads required for the 04-peakcall step","type":"Integer"},"default_adapters_file":{"doc":"Adapters file","type":"File"},"ENCODE_blacklist_bedfile":{"doc":"Bedfile containing ENCODE consensus blacklist regions to be excluded.","type":"File"},"genome_ref_first_index_file":{"doc":"\\\"First index file of Bowtie reference genome with extension 1.ebwt. \\ (Note: the rest of the index files MUST be in the same folder)\\\" ","type":"File"}},"outputs":{"map_pbc_files":{"doc":"PCR Bottleneck Coefficient files (used to flag samples when pbc<0.5)","type":"File[]"},"map_read_count":{"doc":"Read counts of the mapped BAM files","type":"File[]"},"fastq_read_count":{"doc":"Read counts of the (unprocessed) input fastq files","type":"File[]"},"map_bowtie_log_files":{"doc":"Bowtie log file with mapping stats","type":"File[]"},"map_filtered_bam_files":{"doc":"Filtered BAM files (post-processing end point)","type":"File[]"},"quant_bigwig_raw_files":{"doc":"Raw reads bigWig (signal) files","type":"File[]"},"map_filtered_read_count":{"doc":"Read counts of the mapped and filtered BAM files","type":"File[]"},"peak_call_peak_xls_file":{"doc":"Peak calling report file","type":"File[]"},"quant_bigwig_norm_files":{"doc":"Normalized reads bigWig (signal) files","type":"File[]"},"map_preseq_c_curve_files":{"doc":"Preseq c_curve output files","type":"File[]"},"map_percentage_uniq_reads":{"doc":"Percentage of uniq reads from preseq c_curve output","type":"File[]"},"peak_call_narrowpeak_file":{"doc":"Peaks in narrowPeak file format","type":"File[]"},"peak_call_spp_x_cross_corr":{"doc":"SPP strand cross correlation summary","type":"File[]"},"quant_bigwig_extended_files":{"doc":"Fragment extended reads bigWig (signal) files","type":"File[]"},"peak_call_spp_x_cross_corr_plot":{"doc":"SPP strand cross correlation plot","type":"File[]"},"quant_bigwig_extended_norm_files":{"doc":"Normalized fragment extended reads bigWig (signal) files","type":"File[]"},"peak_call_extended_narrowpeak_file":{"doc":"Extended fragment peaks in narrowPeak file format","type":"File[]"},"peak_call_filtered_read_count_file":{"doc":"Filtered read count after peak calling","type":"File[]"},"peak_call_peak_count_within_replicate":{"doc":"Peak counts within replicate","type":"File[]"},"peak_call_read_in_peak_count_within_replicate":{"doc":"Peak counts within replicate","type":"File[]"}},"steps":{"map":{"doc":"DNase-seq 01 mapping - reads: SE","run":"01-map-se.cwl","runType":"WORKFLOW","sources":{"map":{"sourceIDs":["genome_sizes_file"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/DNase-seq_pipeline/pipeline-se.cwl#map/nthreads":{"sourceIDs":["nthreads_map"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/DNase-seq_pipeline/pipeline-se.cwl#map/input_fastq_files":{"sourceIDs":["input_fastq_files"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/DNase-seq_pipeline/pipeline-se.cwl#map/ENCODE_blacklist_bedfile":{"sourceIDs":["ENCODE_blacklist_bedfile"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/DNase-seq_pipeline/pipeline-se.cwl#map/genome_ref_first_index_file":{"sourceIDs":["genome_ref_first_index_file"]}}},"quant":{"doc":"DNase-seq 03 quantification","run":"03-quantification.cwl","runType":"WORKFLOW","sources":{"quant":{"sourceIDs":["genome_sizes_file"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/DNase-seq_pipeline/pipeline-se.cwl#quant/nthreads":{"sourceIDs":["nthreads_quant"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/DNase-seq_pipeline/pipeline-se.cwl#quant/input_bam_files":{"sourceIDs":["map"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/DNase-seq_pipeline/pipeline-se.cwl#quant/input_peak_xls_files":{"sourceIDs":["peak_call"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/DNase-seq_pipeline/pipeline-se.cwl#quant/input_pileup_bedgraphs":{"sourceIDs":["peak_call"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/DNase-seq_pipeline/pipeline-se.cwl#quant/input_read_count_dedup_files":{"sourceIDs":["peak_call"]}}},"peak_call":{"doc":"DNase-seq 02 quantification","run":"02-peakcall.cwl","runType":"WORKFLOW","sources":{"peak_call":{"sourceIDs":["map"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/DNase-seq_pipeline/pipeline-se.cwl#peak_call/nthreads":{"sourceIDs":["nthreads_peakcall"]}}}},"cwltoolVersion":"3.1.20230201224320","visualisationDot":"digraph workflow {\n  graph [\n    bgcolor = \"#eeeeee\"\n    color = \"black\"\n    fontsize = \"10\"\n    labeljust = \"left\"\n    clusterrank = \"local\"\n    ranksep = \"0.22\"\n    nodesep = \"0.05\"\n  ]\n  node [\n    fontname = \"Helvetica\"\n    fontsize = \"10\"\n    fontcolor = \"black\"\n    shape = \"record\"\n    height = \"0\"\n    width = \"0\"\n    color = \"black\"\n    fillcolor = \"lightgoldenrodyellow\"\n    style = \"filled\"\n  ];\n  edge [\n    fontname=\"Helvetica\"\n    fontsize=\"8\"\n    fontcolor=\"black\"\n    color=\"black\"\n    arrowsize=\"0.7\"\n  ];\n  subgraph cluster_inputs {\n    rank = \"same\";\n    style = \"dashed\";\n    label = \"Workflow Inputs\";\n    \"default_adapters_file\" [fillcolor=\"#94DDF4\",label=\"default_adapters_file\"];\n    \"ENCODE_blacklist_bedfile\" [fillcolor=\"#94DDF4\",label=\"ENCODE_blacklist_bedfile\"];\n    \"genome_sizes_file\" [fillcolor=\"#94DDF4\",label=\"genome_sizes_file\"];\n    \"nthreads_peakcall\" [fillcolor=\"#94DDF4\",label=\"nthreads_peakcall\"];\n    \"nthreads_map\" [fillcolor=\"#94DDF4\",label=\"nthreads_map\"];\n    \"nthreads_quant\" [fillcolor=\"#94DDF4\",label=\"nthreads_quant\"];\n    \"genome_ref_first_index_file\" [fillcolor=\"#94DDF4\",label=\"genome_ref_first_index_file\"];\n    \"input_fastq_files\" [fillcolor=\"#94DDF4\",label=\"input_fastq_files\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"map_pbc_files\" [fillcolor=\"#94DDF4\",label=\"map_pbc_files\"];\n    \"map_filtered_read_count\" [fillcolor=\"#94DDF4\",label=\"map_filtered_read_count\"];\n    \"peak_call_extended_narrowpeak_file\" [fillcolor=\"#94DDF4\",label=\"peak_call_extended_narrowpeak_file\"];\n    \"peak_call_read_in_peak_count_within_replicate\" [fillcolor=\"#94DDF4\",label=\"peak_call_read_in_peak_count_within_replicate\"];\n    \"quant_bigwig_extended_files\" [fillcolor=\"#94DDF4\",label=\"quant_bigwig_extended_files\"];\n    \"quant_bigwig_raw_files\" [fillcolor=\"#94DDF4\",label=\"quant_bigwig_raw_files\"];\n    \"map_read_count\" [fillcolor=\"#94DDF4\",label=\"map_read_count\"];\n    \"map_preseq_c_curve_files\" [fillcolor=\"#94DDF4\",label=\"map_preseq_c_curve_files\"];\n    \"peak_call_filtered_read_count_file\" [fillcolor=\"#94DDF4\",label=\"peak_call_filtered_read_count_file\"];\n    \"peak_call_peak_xls_file\" [fillcolor=\"#94DDF4\",label=\"peak_call_peak_xls_file\"];\n    \"map_bowtie_log_files\" [fillcolor=\"#94DDF4\",label=\"map_bowtie_log_files\"];\n    \"map_percentage_uniq_reads\" [fillcolor=\"#94DDF4\",label=\"map_percentage_uniq_reads\"];\n    \"peak_call_peak_count_within_replicate\" [fillcolor=\"#94DDF4\",label=\"peak_call_peak_count_within_replicate\"];\n    \"peak_call_narrowpeak_file\" [fillcolor=\"#94DDF4\",label=\"peak_call_narrowpeak_file\"];\n    \"map_filtered_bam_files\" [fillcolor=\"#94DDF4\",label=\"map_filtered_bam_files\"];\n    \"quant_bigwig_norm_files\" [fillcolor=\"#94DDF4\",label=\"quant_bigwig_norm_files\"];\n    \"fastq_read_count\" [fillcolor=\"#94DDF4\",label=\"fastq_read_count\"];\n    \"peak_call_spp_x_cross_corr\" [fillcolor=\"#94DDF4\",label=\"peak_call_spp_x_cross_corr\"];\n    \"quant_bigwig_extended_norm_files\" [fillcolor=\"#94DDF4\",label=\"quant_bigwig_extended_norm_files\"];\n    \"peak_call_spp_x_cross_corr_plot\" [fillcolor=\"#94DDF4\",label=\"peak_call_spp_x_cross_corr_plot\"];\n  }\n  \"peak_call\" [label=\"peak_call\", fillcolor=\"#F3CEA1\"];\n  \"map\" [label=\"map\", fillcolor=\"#F3CEA1\"];\n  \"quant\" [label=\"quant\", fillcolor=\"#F3CEA1\"];\n  \"map\" -> \"peak_call\" [label=\"input_bam_files\"];\n  \"nthreads_peakcall\" -> \"peak_call\" [label=\"nthreads\"];\n  \"genome_sizes_file\" -> \"map\" [label=\"genome_sizes_file\"];\n  \"genome_ref_first_index_file\" -> \"map\" [label=\"genome_ref_first_index_file\"];\n  \"nthreads_map\" -> \"map\" [label=\"nthreads\"];\n  \"input_fastq_files\" -> \"map\" [label=\"input_fastq_files\"];\n  \"ENCODE_blacklist_bedfile\" -> \"map\" [label=\"ENCODE_blacklist_bedfile\"];\n  \"genome_sizes_file\" -> \"quant\" [label=\"input_genome_sizes\"];\n  \"peak_call\" -> \"quant\" [label=\"input_read_count_dedup_files\"];\n  \"peak_call\" -> \"quant\" [label=\"input_peak_xls_files\"];\n  \"peak_call\" -> \"quant\" [label=\"input_pileup_bedgraphs\"];\n  \"nthreads_quant\" -> \"quant\" [label=\"nthreads\"];\n  \"map\" -> \"quant\" [label=\"input_bam_files\"];\n  \"map\" -> \"map_pbc_files\";\n  \"map\" -> \"map_filtered_read_count\";\n  \"peak_call\" -> \"peak_call_extended_narrowpeak_file\";\n  \"peak_call\" -> \"peak_call_read_in_peak_count_within_replicate\";\n  \"quant\" -> \"quant_bigwig_extended_files\";\n  \"quant\" -> \"quant_bigwig_raw_files\";\n  \"map\" -> \"map_read_count\";\n  \"map\" -> \"map_preseq_c_curve_files\";\n  \"peak_call\" -> \"peak_call_filtered_read_count_file\";\n  \"peak_call\" -> \"peak_call_peak_xls_file\";\n  \"map\" -> \"map_bowtie_log_files\";\n  \"map\" -> \"map_percentage_uniq_reads\";\n  \"peak_call\" -> \"peak_call_peak_count_within_replicate\";\n  \"peak_call\" -> \"peak_call_narrowpeak_file\";\n  \"map\" -> \"map_filtered_bam_files\";\n  \"quant\" -> \"quant_bigwig_norm_files\";\n  \"map\" -> \"fastq_read_count\";\n  \"peak_call\" -> \"peak_call_spp_x_cross_corr\";\n  \"quant\" -> \"quant_bigwig_extended_norm_files\";\n  \"peak_call\" -> \"peak_call_spp_x_cross_corr_plot\";\n}\n","licenseLink":"https://spdx.org/licenses/MIT","permalink":"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/DNase-seq_pipeline/pipeline-se.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/alexbarrera/GGR-cwl/blob/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/DNase-seq_pipeline/pipeline-se.cwl","visualisationPng":"/graph/png/github.com/alexbarrera/GGR-cwl/blob/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/DNase-seq_pipeline/pipeline-se.cwl","visualisationSvg":"/graph/svg/github.com/alexbarrera/GGR-cwl/blob/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/DNase-seq_pipeline/pipeline-se.cwl","roBundle":"/robundle/github.com/alexbarrera/GGR-cwl/blob/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/DNase-seq_pipeline/pipeline-se.cwl","licenseName":"MIT License"}