{"@id":"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/03-map-se.cwl","retrievedFrom":{"repoUrl":"https://github.com/alexbarrera/GGR-cwl.git","branch":"81555a89cc2d16bd3ab131a6685a44b44f08f927","path":"v1.0/ATAC-seq_pipeline/03-map-se.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/alexbarrera/GGR-cwl/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/03-map-se.cwl","url":"https://github.com/alexbarrera/GGR-cwl/blob/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/03-map-se.cwl"},"retrievedOn":"2026-09-25T18:14:44.492+00:00","lastCommit":"81555a89cc2d16bd3ab131a6685a44b44f08f927","label":"03-map-se.cwl","doc":"ATAC-seq 03 mapping - reads: SE","inputs":{"nthreads":{"type":"Integer"},"picard_jar_path":{"doc":"Picard Java jar file","type":"String"},"picard_java_opts":{"doc":"JVM arguments should be a quoted, space separated list (e.g. \\\"-Xms128m -Xmx512m\\\")","type":"String (Optional)"},"genome_sizes_file":{"doc":"Genome sizes tab-delimited file (used in samtools)","type":"File"},"input_fastq_files":{"doc":"Input fastq files","type":"File[]"},"genome_ref_first_index_file":{"doc":"Bowtie first index files for reference genome (e.g. *1.ebwt). The rest of the files should be in the same folder.","type":"File"}},"outputs":{"output_pbc_files":{"doc":"PCR Bottleneck Coeficient files.","type":"File[]"},"output_bowtie_log":{"doc":"Bowtie log file.","type":"File[]"},"output_read_count_mapped":{"doc":"Read counts of the mapped BAM files","type":"File[]"},"output_preseq_c_curve_files":{"doc":"Preseq c_curve output files.","type":"File[]"},"output_percentage_uniq_reads":{"doc":"Percentage of uniq reads from preseq c_curve output","type":"File[]"},"output_read_count_mapped_filtered":{"doc":"Read counts of the mapped and filtered BAM files","type":"File[]"},"output_data_sorted_dedup_bam_files":{"doc":"BAM files without duplicate reads.","type":"File[]"},"output_percent_mitochondrial_reads":{"doc":"Percentage of mitochondrial reads.","type":"File[]"},"output_picard_mark_duplicates_files":{"doc":"Picard MarkDuplicates metrics files.","type":"File[]"},"output_data_sorted_dups_marked_bam_files":{"doc":"BAM files with marked duplicate reads.","type":"File[]"}},"steps":{"sam2bam":{"run":"../map/samtools2bam.cwl","runType":"COMMANDLINETOOL","sources":{"sam2bam":{"sourceIDs":["nthreads"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/03-map-se.cwl#sam2bam/input_file":{"sourceIDs":["bowtie-se"]}}},"bowtie-se":{"run":"../map/bowtie-se.cwl","runType":"COMMANDLINETOOL","sources":{"bowtie-se":{"sourceIDs":["input_fastq_files"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/03-map-se.cwl#bowtie-se/nthreads":{"sourceIDs":["nthreads"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/03-map-se.cwl#bowtie-se/output_filename":{"sourceIDs":["extract_basename_2"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/03-map-se.cwl#bowtie-se/genome_ref_first_index_file":{"sourceIDs":["genome_ref_first_index_file"]}}},"sort_bams":{"run":"../map/samtools-sort.cwl","runType":"COMMANDLINETOOL","sources":{"sort_bams":{"sourceIDs":["sam2bam"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/03-map-se.cwl#sort_bams/nthreads":{"sourceIDs":["nthreads"]}}},"index_bams":{"run":"../map/samtools-index.cwl","runType":"COMMANDLINETOOL","sources":{"index_bams":{"sourceIDs":["sort_bams"]}}},"bam_idxstats":{"run":"../map/samtools-idxstats.cwl","runType":"COMMANDLINETOOL","sources":{"bam_idxstats":{"sourceIDs":["index_bams"]}}},"preseq-c-curve":{"doc":"Usage: c_curve [OPTIONS] <sorted-bed-file>\n\nOptions:\n  -o, -output   yield output file (default: stdout) \n  -s, -step     step size in extrapolations (default: 1e+06) \n  -v, -verbose  print more information \n  -P, -pe       input is paired end read file \n  -H, -hist     input is a text file containing the observed histogram \n  -V, -vals     input is a text file containing only the observed counts \n  -B, -bam      input is in BAM format \n  -l, -seg_len  maximum segment length when merging paired end bam reads \n                (default: 5000) \n\nHelp options:\n  -?, -help     print this help message \n      -about    print about message","run":"../map/preseq-c_curve.cwl","runType":"COMMANDLINETOOL","sources":{"preseq-c-curve":{"sourceIDs":["filtered2sorted"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/03-map-se.cwl#preseq-c-curve/output_file_basename":{"sourceIDs":["extract_basename_2"]}}},"filter-unmapped":{"run":"../map/samtools-filter-unmapped.cwl","runType":"COMMANDLINETOOL","sources":{"filter-unmapped":{"sourceIDs":["sort_bams"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/03-map-se.cwl#filter-unmapped/output_filename":{"sourceIDs":["extract_basename_2"]}}},"filtered2sorted":{"run":"../map/samtools-sort.cwl","runType":"COMMANDLINETOOL","sources":{"filtered2sorted":{"sourceIDs":["nthreads"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/03-map-se.cwl#filtered2sorted/input_file":{"sourceIDs":["filter-unmapped"]}}},"mark_duplicates":{"run":"../map/picard-MarkDuplicates.cwl","runType":"COMMANDLINETOOL","sources":{"mark_duplicates":{"sourceIDs":["picard_java_opts"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/03-map-se.cwl#mark_duplicates/input_file":{"sourceIDs":["index_filtered_bam"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/03-map-se.cwl#mark_duplicates/output_filename":{"sourceIDs":["extract_basename_2"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/03-map-se.cwl#mark_duplicates/picard_jar_path":{"sourceIDs":["picard_jar_path"]}}},"sort_dedup_bams":{"run":"../map/samtools-sort.cwl","runType":"COMMANDLINETOOL","sources":{"sort_dedup_bams":{"sourceIDs":["remove_duplicates"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/03-map-se.cwl#sort_dedup_bams/nthreads":{"sourceIDs":["nthreads"]}}},"index_dedup_bams":{"run":"../map/samtools-index.cwl","runType":"COMMANDLINETOOL","sources":{"index_dedup_bams":{"sourceIDs":["sort_dedup_bams"]}}},"remove_duplicates":{"run":"../map/samtools-view.cwl","runType":"COMMANDLINETOOL","sources":{"remove_duplicates":{"sourceIDs":["index_dups_marked_bams"]}}},"extract_basename_1":{"doc":"Extracts the base name of a file","run":"../utils/extract-basename.cwl","runType":"COMMANDLINETOOL","sources":{"extract_basename_1":{"sourceIDs":["input_fastq_files"]}}},"extract_basename_2":{"doc":"Extracts the base name of a file","run":"../utils/remove-extension.cwl","runType":"COMMANDLINETOOL","sources":{"extract_basename_2":{"sourceIDs":["extract_basename_1"]}}},"index_filtered_bam":{"run":"../map/samtools-index.cwl","runType":"COMMANDLINETOOL","sources":{"index_filtered_bam":{"sourceIDs":["filtered2sorted"]}}},"mapped_reads_count":{"doc":"Get number of processed reads from Bowtie log.","run":"../map/bowtie-log-read-count.cwl","runType":"COMMANDLINETOOL","sources":{"mapped_reads_count":{"sourceIDs":["bowtie-se"]}}},"percent_uniq_reads":{"doc":"Get number of processed reads from Bowtie log.","run":"../map/preseq-percent-uniq-reads.cwl","runType":"COMMANDLINETOOL","sources":{"percent_uniq_reads":{"sourceIDs":["preseq-c-curve"]}}},"sort_dups_marked_bams":{"run":"../map/samtools-sort.cwl","runType":"COMMANDLINETOOL","sources":{"sort_dups_marked_bams":{"sourceIDs":["nthreads"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/03-map-se.cwl#sort_dups_marked_bams/input_file":{"sourceIDs":["mark_duplicates"]}}},"index_dups_marked_bams":{"run":"../map/samtools-index.cwl","runType":"COMMANDLINETOOL","sources":{"index_dups_marked_bams":{"sourceIDs":["sort_dups_marked_bams"]}}},"execute_pcr_bottleneck_coef":{"doc":"ChIP-seq - map - PCR Bottleneck Coefficients","run":"../map/pcr-bottleneck-coef.cwl","runType":"WORKFLOW","sources":{"execute_pcr_bottleneck_coef":{"sourceIDs":["extract_basename_2"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/03-map-se.cwl#execute_pcr_bottleneck_coef/genome_sizes":{"sourceIDs":["genome_sizes_file"]},"https://w3id.org/cwl/view/git/81555a89cc2d16bd3ab131a6685a44b44f08f927/v1.0/ATAC-seq_pipeline/03-map-se.cwl#execute_pcr_bottleneck_coef/input_bam_files":{"sourceIDs":["filtered2sorted"]}}},"mapped_filtered_reads_count":{"doc":"Extract mapped reads from BAM file using Samtools flagstat command","run":"../peak_calling/samtools-extract-number-mapped-reads.cwl","runType":"COMMANDLINETOOL","sources":{"mapped_filtered_reads_count":{"sourceIDs":["sort_dedup_bams"]}}},"percent_mitochondrial_reads":{"run":"../utils/idxstats-percentage-of-reads-in-chrom.cwl","runType":"EXPRESSIONTOOL","sources":{"percent_mitochondrial_reads":{"sourceIDs":["bam_idxstats"]}}}},"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    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[label=\"input_fastq_file\"];\n  \"extract_basename_2\" -> \"bowtie-se\" [label=\"output_filename\"];\n  \"genome_ref_first_index_file\" -> \"bowtie-se\" [label=\"genome_ref_first_index_file\"];\n  \"nthreads\" -> \"bowtie-se\" [label=\"nthreads\"];\n  \"nthreads\" -> \"sam2bam\" [label=\"nthreads\"];\n  \"bowtie-se\" -> \"sam2bam\" [label=\"input_file\"];\n  \"filtered2sorted\" -> \"preseq-c-curve\" [label=\"input_sorted_file\"];\n  \"extract_basename_2\" -> \"preseq-c-curve\" [label=\"output_file_basename\"];\n  \"index_bams\" -> \"bam_idxstats\" [label=\"bam\"];\n  \"sort_dups_marked_bams\" -> \"index_dups_marked_bams\" [label=\"input_file\"];\n  \"extract_basename_1\" -> \"extract_basename_2\" [label=\"file_path\"];\n  \"preseq-c-curve\" -> \"percent_uniq_reads\" [label=\"preseq_c_curve_outfile\"];\n  \"bam_idxstats\" -> \"percent_mitochondrial_reads\" [label=\"idxstats\"];\n  \"filtered2sorted\" -> \"index_filtered_bam\" [label=\"input_file\"];\n  \"sort_bams\" -> \"filter-unmapped\" [label=\"input_file\"];\n  \"extract_basename_2\" -> \"filter-unmapped\" [label=\"output_filename\"];\n  \"picard_java_opts\" -> \"mark_duplicates\" [label=\"java_opts\"];\n  \"extract_basename_2\" -> \"mark_duplicates\" [label=\"output_filename\"];\n  \"picard_jar_path\" -> \"mark_duplicates\" [label=\"picard_jar_path\"];\n  \"index_filtered_bam\" -> \"mark_duplicates\" [label=\"input_file\"];\n  \"input_fastq_files\" -> \"extract_basename_1\" [label=\"input_file\"];\n  \"remove_duplicates\" -> \"sort_dedup_bams\" [label=\"input_file\"];\n  \"nthreads\" -> \"sort_dedup_bams\" [label=\"nthreads\"];\n  \"bowtie-se\" -> \"mapped_reads_count\" [label=\"bowtie_log\"];\n  \"index_dups_marked_bams\" -> \"remove_duplicates\" [label=\"input_file\"];\n  \"mapped_filtered_reads_count\" -> \"output_read_count_mapped_filtered\";\n  \"execute_pcr_bottleneck_coef\" -> \"output_pbc_files\";\n  \"bowtie-se\" -> \"output_bowtie_log\";\n  \"index_dedup_bams\" -> 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