{"@id":"https://w3id.org/cwl/view/git/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_chimeric_se.cwl","retrievedFrom":{"repoUrl":"https://github.com/YeoLab/eclip.git","branch":"c0fffc4979a92371dc0667a03e3d957bf7f77600","path":"cwl/wf_trim_and_map_chimeric_se.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/YeoLab/eclip/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_chimeric_se.cwl","url":"https://github.com/YeoLab/eclip/blob/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_chimeric_se.cwl"},"retrievedOn":"2023-06-27T16:23:33.743+00:00","lastCommit":"c0fffc4979a92371dc0667a03e3d957bf7f77600","label":"wf_trim_and_map_chimeric_se.cwl","doc":"This workflow takes in appropriate trimming params and demultiplexed reads,\nand performs the following steps in order: trimx1, trimx2, fastq-sort, filter repeat elements, fastq-sort, genomic mapping, sort alignment, index alignment, namesort, PCR dedup, sort alignment, index alignment\n","inputs":{"read1":{"type":"File"},"read_name":{"type":"String"},"a_adapters":{"type":"File"},"bam_suffix":{"type":"String"},"sort_names":{"type":"Boolean"},"trim_times":{"type":"String"},"dataset_name":{"type":"String"},"fastq_suffix":{"type":"String"},"trim_error_rate":{"type":"String"},"hard_trim_length":{"type":"Integer"},"speciesGenomeDir":{"type":"Directory"},"repeatElementGenomeDir":{"type":"Directory"},"trimagain_overlap_length":{"type":"String"},"trimfirst_overlap_length":{"type":"String"}},"outputs":{"A_output_sorted_bam":{"type":"File"},"X_output_sorted_bam":{"type":"File"},"X_output_trim_again":{"type":"File[]"},"X_output_trim_first":{"type":"File[]"},"A_output_mapgenome_stats":{"type":"File"},"A_output_maprepeats_stats":{"type":"File"},"X_output_trim_again_metrics":{"type":"File"},"X_output_trim_first_metrics":{"type":"File"},"X_output_barcodecollapsese_bam":{"type":"File"},"A_output_sort_repunmapped_fastq":{"type":"File"},"A_output_mapgenome_star_settings":{"type":"File"},"X_output_trim_again_fastqc_stats":{"type":"File"},"X_output_trim_first_fastqc_stats":{"type":"File"},"A_output_maprepeats_star_settings":{"type":"File"},"X_output_trim_again_fastqc_report":{"type":"File"},"X_output_trim_first_fastqc_report":{"type":"File"},"X_output_barcodecollapsese_metrics":{"type":"File"},"A_output_mapgenome_mapped_to_genome":{"type":"File"},"A_output_maprepeats_mapped_to_genome":{"type":"File"}},"steps":{"A_sort":{"doc":"This tool wraps samtools sort by coordinates (namesort flag is False by default).\n  Usage: samtools sort [options...] [in.bam]\n","run":"sort.cwl","runType":"COMMANDLINETOOL","sources":{"A_sort":{"sourceIDs":["X_sortlexico"]}}},"X_sort":{"doc":"This tool wraps samtools sort by coordinates (namesort flag is False by default).\n  Usage: samtools sort [options...] [in.bam]\n","run":"sort.cwl","runType":"COMMANDLINETOOL","sources":{"X_sort":{"sourceIDs":["X_barcodecollapsese"]}}},"X_trim":{"doc":"This tool wraps cutadapt with default parameters set to single-end eCLIP processing defaults.\n  Usage: cutadapt -a ADAPT1 -A ADAPT2 [options] -o out1.fastq -p out2.fastq in1.fastq in2.fastq\n","run":"trim_se.cwl","runType":"COMMANDLINETOOL","sources":{"X_trim":{"sourceIDs":["get_a_adapters"]},"https://w3id.org/cwl/view/git/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_chimeric_se.cwl#X_trim/times":{"sourceIDs":["trim_times"]},"https://w3id.org/cwl/view/git/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_chimeric_se.cwl#X_trim/error_rate":{"sourceIDs":["trim_error_rate"]},"https://w3id.org/cwl/view/git/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_chimeric_se.cwl#X_trim/input_trim":{"sourceIDs":["read1"]},"https://w3id.org/cwl/view/git/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_chimeric_se.cwl#X_trim/input_trim_overlap_length":{"sourceIDs":["trimfirst_overlap_length"]}}},"A_index":{"doc":"samtools-index.cwl is developed for CWL consortium\n","run":"samtools-index.cwl","runType":"COMMANDLINETOOL","sources":{"A_index":{"sourceIDs":["A_sort"]}}},"X_trim_umi":{"doc":"This tool wraps cutadapt to trim off the 3' end of R1 (may be UMIs) for eCLASH reads","run":"trim_umi.cwl","runType":"COMMANDLINETOOL","sources":{"X_trim_umi":{"sourceIDs":["X_trim_again"]},"https://w3id.org/cwl/view/git/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_chimeric_se.cwl#X_trim_umi/hard_trim_length":{"sourceIDs":["hard_trim_length"]}}},"A_map_genome":{"run":"star-genome.cwl","runType":"COMMANDLINETOOL","sources":{"A_map_genome":{"sourceIDs":["A_sort_repunmapped_fastq"]},"https://w3id.org/cwl/view/git/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_chimeric_se.cwl#A_map_genome/genomeDir":{"sourceIDs":["speciesGenomeDir"]}}},"X_sortlexico":{"doc":"This tool wraps samtools sort, setting the by-name (-n) flag to be True by default.\n  Usage: samtools sort -n <input.bam> <output.bam>\n","run":"namesort.cwl","runType":"COMMANDLINETOOL","sources":{"X_sortlexico":{"sourceIDs":["sort_names"]},"https://w3id.org/cwl/view/git/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_chimeric_se.cwl#X_sortlexico/input_sort_bam":{"sourceIDs":["rename_mapped_genome"]}}},"X_trim_again":{"doc":"This tool wraps cutadapt with default parameters set to single-end eCLIP processing defaults.\n  Usage: cutadapt -a ADAPT1 -A ADAPT2 [options] -o out1.fastq -p out2.fastq in1.fastq in2.fastq\n","run":"trim_se.cwl","runType":"COMMANDLINETOOL","sources":{"X_trim_again":{"sourceIDs":["trim_times"]},"https://w3id.org/cwl/view/git/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_chimeric_se.cwl#X_trim_again/error_rate":{"sourceIDs":["trim_error_rate"]},"https://w3id.org/cwl/view/git/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_chimeric_se.cwl#X_trim_again/input_trim":{"sourceIDs":["X_trim"]},"https://w3id.org/cwl/view/git/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_chimeric_se.cwl#X_trim_again/input_trim_a_adapters":{"sourceIDs":["get_a_adapters"]},"https://w3id.org/cwl/view/git/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_chimeric_se.cwl#X_trim_again/input_trim_overlap_length":{"sourceIDs":["trimagain_overlap_length"]}}},"A_map_repeats":{"run":"star-repeatmapping.cwl","runType":"COMMANDLINETOOL","sources":{"A_map_repeats":{"sourceIDs":["repeatElementGenomeDir"]},"https://w3id.org/cwl/view/git/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_chimeric_se.cwl#A_map_repeats/readFilesIn":{"sourceIDs":["X_trim_umi"]}}},"get_a_adapters":{"doc":"Returns string array expression based on lines in a fasta file (SKIPS >).","run":"file2stringArray.cwl","runType":"EXPRESSIONTOOL","sources":{"get_a_adapters":{"sourceIDs":["a_adapters"]}}},"index_rmdup_bam":{"doc":"samtools-index.cwl is developed for CWL consortium\n","run":"samtools-index.cwl","runType":"COMMANDLINETOOL","sources":{"index_rmdup_bam":{"sourceIDs":["X_sort"]}}},"step_fastqc_trim":{"doc":"This workflow takes in single-end reads, and performs the following steps in order:\ndemux_se.cwl (does not actually demux for single end, but mirrors the paired-end processing protocol)\n","run":"wf_fastqc.cwl","runType":"WORKFLOW","sources":{"step_fastqc_trim":{"sourceIDs":["step_gzip_sort_X_trim"]}}},"step_gzip_trim_umi":{"run":"gzip.cwl","runType":"COMMANDLINETOOL","sources":{"step_gzip_trim_umi":{"sourceIDs":["X_trim_umi"]}}},"X_barcodecollapsese":{"doc":"The purpose of this command is to deduplicate BAM files based\non the first mapping co-ordinate and the UMI attached to the read.\nIt is assumed that the FASTQ files were processed with extract_umi.py\nbefore mapping and thus the UMI is the last word of the read name. e.g:\n\n@HISEQ:87:00000000_AATT\n\nwhere AATT is the UMI sequeuence.\n\n  Usage: umi_tools dedup -I infile.bam -S deduped.bam -L dedup.log\n","run":"barcodecollapse_se.cwl","runType":"COMMANDLINETOOL","sources":{"X_barcodecollapsese":{"sourceIDs":["A_index"]}}},"A_sort_trimmed_fastq":{"doc":"Sorts FASTQ files by their read name. Sorted fastq files are required to keep mapping steps\ndeterministic.\n\n  Usage: fastq-sort --id FASTQ_FILE > STDOUT\n","run":"fastqsort.cwl","runType":"COMMANDLINETOOL","sources":{"A_sort_trimmed_fastq":{"sourceIDs":["X_trim_again"]}}},"rename_mapped_genome":{"run":"rename.cwl","runType":"COMMANDLINETOOL","sources":{"rename_mapped_genome":{"defaultVal":"\\\".bam\\\""},"https://w3id.org/cwl/view/git/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_chimeric_se.cwl#rename_mapped_genome/newname":{"sourceIDs":["read1"]},"https://w3id.org/cwl/view/git/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_chimeric_se.cwl#rename_mapped_genome/srcfile":{"sourceIDs":["A_map_genome"]}}},"rename_mapped_repeats":{"run":"rename.cwl","runType":"COMMANDLINETOOL","sources":{"rename_mapped_repeats":{"defaultVal":"\\\".bam\\\""},"https://w3id.org/cwl/view/git/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_chimeric_se.cwl#rename_mapped_repeats/newname":{"sourceIDs":["read1"]},"https://w3id.org/cwl/view/git/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_chimeric_se.cwl#rename_mapped_repeats/srcfile":{"sourceIDs":["A_map_repeats"]}}},"step_gzip_sort_X_trim":{"run":"gzip.cwl","runType":"COMMANDLINETOOL","sources":{"step_gzip_sort_X_trim":{"sourceIDs":["X_trim"]}}},"step_fastqc_trim_again":{"doc":"This workflow takes in single-end reads, and performs the following steps in order:\ndemux_se.cwl (does not actually demux for single end, but mirrors the paired-end processing protocol)\n","run":"wf_fastqc.cwl","runType":"WORKFLOW","sources":{"step_fastqc_trim_again":{"sourceIDs":["step_gzip_sort_X_trim_again"]}}},"rename_unmapped_repeats":{"run":"rename.cwl","runType":"COMMANDLINETOOL","sources":{"rename_unmapped_repeats":{"defaultVal":"\\\".fq\\\""},"https://w3id.org/cwl/view/git/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_chimeric_se.cwl#rename_unmapped_repeats/newname":{"sourceIDs":["read1"]},"https://w3id.org/cwl/view/git/c0fffc4979a92371dc0667a03e3d957bf7f77600/cwl/wf_trim_and_map_chimeric_se.cwl#rename_unmapped_repeats/srcfile":{"sourceIDs":["A_map_repeats"]}}},"A_sort_repunmapped_fastq":{"doc":"Sorts FASTQ files by their read name. Sorted fastq files are required to keep mapping steps\ndeterministic.\n\n  Usage: fastq-sort --id FASTQ_FILE > STDOUT\n","run":"fastqsort.cwl","runType":"COMMANDLINETOOL","sources":{"A_sort_repunmapped_fastq":{"sourceIDs":["rename_unmapped_repeats"]}}},"step_gzip_sort_X_trim_again":{"run":"gzip.cwl","runType":"COMMANDLINETOOL","sources":{"step_gzip_sort_X_trim_again":{"sourceIDs":["A_sort_trimmed_fastq"]}}},"step_gzip_sort_repunmapped_fastq":{"run":"gzip.cwl","runType":"COMMANDLINETOOL","sources":{"step_gzip_sort_repunmapped_fastq":{"sourceIDs":["A_sort_repunmapped_fastq"]}}}},"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    \"hard_trim_length\" [fillcolor=\"#94DDF4\",label=\"hard_trim_length\"];\n    \"read1\" [fillcolor=\"#94DDF4\",label=\"read1\"];\n    \"speciesGenomeDir\" [fillcolor=\"#94DDF4\",label=\"speciesGenomeDir\"];\n    \"trim_error_rate\" [fillcolor=\"#94DDF4\",label=\"trim_error_rate\"];\n    \"a_adapters\" [fillcolor=\"#94DDF4\",label=\"a_adapters\"];\n    \"fastq_suffix\" [fillcolor=\"#94DDF4\",label=\"fastq_suffix\"];\n    \"read_name\" [fillcolor=\"#94DDF4\",label=\"read_name\"];\n    \"repeatElementGenomeDir\" [fillcolor=\"#94DDF4\",label=\"repeatElementGenomeDir\"];\n    \"trim_times\" [fillcolor=\"#94DDF4\",label=\"trim_times\"];\n    \"bam_suffix\" [fillcolor=\"#94DDF4\",label=\"bam_suffix\"];\n    \"trimagain_overlap_length\" [fillcolor=\"#94DDF4\",label=\"trimagain_overlap_length\"];\n    \"trimfirst_overlap_length\" [fillcolor=\"#94DDF4\",label=\"trimfirst_overlap_length\"];\n    \"dataset_name\" [fillcolor=\"#94DDF4\",label=\"dataset_name\"];\n    \"sort_names\" [fillcolor=\"#94DDF4\",label=\"sort_names\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"A_output_maprepeats_star_settings\" [fillcolor=\"#94DDF4\",label=\"A_output_maprepeats_star_settings\"];\n    \"A_output_mapgenome_star_settings\" [fillcolor=\"#94DDF4\",label=\"A_output_mapgenome_star_settings\"];\n    \"A_output_sorted_bam\" [fillcolor=\"#94DDF4\",label=\"A_output_sorted_bam\"];\n    \"X_output_trim_first_fastqc_report\" [fillcolor=\"#94DDF4\",label=\"X_output_trim_first_fastqc_report\"];\n    \"A_output_sort_repunmapped_fastq\" [fillcolor=\"#94DDF4\",label=\"A_output_sort_repunmapped_fastq\"];\n    \"A_output_maprepeats_stats\" [fillcolor=\"#94DDF4\",label=\"A_output_maprepeats_stats\"];\n    \"X_output_trim_again\" [fillcolor=\"#94DDF4\",label=\"X_output_trim_again\"];\n    \"A_output_mapgenome_stats\" [fillcolor=\"#94DDF4\",label=\"A_output_mapgenome_stats\"];\n    \"X_output_trim_first_fastqc_stats\" [fillcolor=\"#94DDF4\",label=\"X_output_trim_first_fastqc_stats\"];\n    \"X_output_trim_again_fastqc_stats\" [fillcolor=\"#94DDF4\",label=\"X_output_trim_again_fastqc_stats\"];\n    \"X_output_trim_again_fastqc_report\" [fillcolor=\"#94DDF4\",label=\"X_output_trim_again_fastqc_report\"];\n    \"X_output_trim_again_metrics\" [fillcolor=\"#94DDF4\",label=\"X_output_trim_again_metrics\"];\n    \"X_output_barcodecollapsese_bam\" [fillcolor=\"#94DDF4\",label=\"X_output_barcodecollapsese_bam\"];\n    \"X_output_barcodecollapsese_metrics\" [fillcolor=\"#94DDF4\",label=\"X_output_barcodecollapsese_metrics\"];\n    \"X_output_trim_first_metrics\" [fillcolor=\"#94DDF4\",label=\"X_output_trim_first_metrics\"];\n    \"X_output_sorted_bam\" [fillcolor=\"#94DDF4\",label=\"X_output_sorted_bam\"];\n    \"X_output_trim_first\" [fillcolor=\"#94DDF4\",label=\"X_output_trim_first\"];\n    \"A_output_mapgenome_mapped_to_genome\" [fillcolor=\"#94DDF4\",label=\"A_output_mapgenome_mapped_to_genome\"];\n    \"A_output_maprepeats_mapped_to_genome\" [fillcolor=\"#94DDF4\",label=\"A_output_maprepeats_mapped_to_genome\"];\n  }\n  \"rename_mapped_genome\" [label=\"rename_mapped_genome\"];\n  \"X_sort\" [label=\"X_sort\"];\n  \"rename_mapped_repeats\" [label=\"rename_mapped_repeats\"];\n  \"index_rmdup_bam\" [label=\"index_rmdup_bam\"];\n  \"A_index\" [label=\"A_index\"];\n  \"A_sort_trimmed_fastq\" [label=\"A_sort_trimmed_fastq\"];\n  \"A_map_genome\" [label=\"A_map_genome\"];\n  \"X_trim_umi\" [label=\"X_trim_umi\"];\n  \"step_gzip_sort_repunmapped_fastq\" [label=\"step_gzip_sort_repunmapped_fastq\"];\n  \"X_sortlexico\" [label=\"X_sortlexico\"];\n  \"X_barcodecollapsese\" [label=\"X_barcodecollapsese\"];\n  \"step_fastqc_trim_again\" [label=\"step_fastqc_trim_again\", fillcolor=\"#F3CEA1\"];\n  \"step_gzip_sort_X_trim_again\" [label=\"step_gzip_sort_X_trim_again\"];\n  \"step_gzip_sort_X_trim\" [label=\"step_gzip_sort_X_trim\"];\n  \"A_sort\" [label=\"A_sort\"];\n  \"A_sort_repunmapped_fastq\" [label=\"A_sort_repunmapped_fastq\"];\n  \"get_a_adapters\" [label=\"get_a_adapters\"];\n  \"rename_unmapped_repeats\" [label=\"rename_unmapped_repeats\"];\n  \"X_trim\" [label=\"X_trim\"];\n  \"step_gzip_trim_umi\" [label=\"step_gzip_trim_umi\"];\n  \"step_fastqc_trim\" [label=\"step_fastqc_trim\", fillcolor=\"#F3CEA1\"];\n  \"X_trim_again\" [label=\"X_trim_again\"];\n  \"A_map_repeats\" [label=\"A_map_repeats\"];\n  \"default1\" -> \"rename_mapped_genome\" [label=\"suffix\"];\n  \"default1\" [label=\"\\\".bam\\\"\", fillcolor=\"#D5AEFC\"];\n  \"A_map_genome\" -> \"rename_mapped_genome\" [label=\"srcfile\"];\n  \"read1\" -> \"rename_mapped_genome\" [label=\"newname\"];\n  \"X_barcodecollapsese\" -> \"X_sort\" [label=\"input_sort_bam\"];\n  \"default2\" -> \"rename_mapped_repeats\" [label=\"suffix\"];\n  \"default2\" [label=\"\\\".bam\\\"\", fillcolor=\"#D5AEFC\"];\n  \"A_map_repeats\" -> \"rename_mapped_repeats\" [label=\"srcfile\"];\n  \"read1\" -> \"rename_mapped_repeats\" [label=\"newname\"];\n  \"X_sort\" -> \"index_rmdup_bam\" [label=\"alignments\"];\n  \"A_sort\" -> \"A_index\" [label=\"alignments\"];\n  \"X_trim_again\" -> \"A_sort_trimmed_fastq\" [label=\"input_fastqsort_fastq\"];\n  \"A_sort_repunmapped_fastq\" -> \"A_map_genome\" [label=\"readFilesIn\"];\n  \"speciesGenomeDir\" -> \"A_map_genome\" [label=\"genomeDir\"];\n  \"X_trim_again\" -> \"X_trim_umi\" [label=\"input_trim\"];\n  \"hard_trim_length\" -> \"X_trim_umi\" [label=\"hard_trim_length\"];\n  \"A_sort_repunmapped_fastq\" -> \"step_gzip_sort_repunmapped_fastq\" [label=\"input\"];\n  \"sort_names\" -> \"X_sortlexico\" [label=\"name_sort\"];\n  \"rename_mapped_genome\" -> \"X_sortlexico\" [label=\"input_sort_bam\"];\n  \"A_index\" -> \"X_barcodecollapsese\" [label=\"input_barcodecollapsese_bam\"];\n  \"step_gzip_sort_X_trim_again\" -> \"step_fastqc_trim_again\" [label=\"reads\"];\n  \"A_sort_trimmed_fastq\" -> \"step_gzip_sort_X_trim_again\" [label=\"input\"];\n  \"X_trim\" -> \"step_gzip_sort_X_trim\" [label=\"input\"];\n  \"X_sortlexico\" -> \"A_sort\" [label=\"input_sort_bam\"];\n  \"rename_unmapped_repeats\" -> \"A_sort_repunmapped_fastq\" [label=\"input_fastqsort_fastq\"];\n  \"a_adapters\" -> \"get_a_adapters\" [label=\"file\"];\n  \"default3\" -> \"rename_unmapped_repeats\" [label=\"suffix\"];\n  \"default3\" [label=\"\\\".fq\\\"\", fillcolor=\"#D5AEFC\"];\n  \"read1\" -> \"rename_unmapped_repeats\" [label=\"newname\"];\n  \"A_map_repeats\" -> \"rename_unmapped_repeats\" [label=\"srcfile\"];\n  \"get_a_adapters\" -> \"X_trim\" [label=\"input_trim_a_adapters\"];\n  \"trim_error_rate\" -> \"X_trim\" [label=\"error_rate\"];\n  \"trim_times\" -> \"X_trim\" [label=\"times\"];\n  \"trimfirst_overlap_length\" -> \"X_trim\" [label=\"input_trim_overlap_length\"];\n  \"read1\" -> \"X_trim\" [label=\"input_trim\"];\n  \"X_trim_umi\" -> \"step_gzip_trim_umi\" [label=\"input\"];\n  \"step_gzip_sort_X_trim\" -> \"step_fastqc_trim\" [label=\"reads\"];\n  \"trim_times\" -> \"X_trim_again\" [label=\"times\"];\n  \"trim_error_rate\" -> \"X_trim_again\" [label=\"error_rate\"];\n  \"trimagain_overlap_length\" -> \"X_trim_again\" [label=\"input_trim_overlap_length\"];\n  \"get_a_adapters\" -> \"X_trim_again\" [label=\"input_trim_a_adapters\"];\n  \"X_trim\" -> \"X_trim_again\" [label=\"input_trim\"];\n  \"repeatElementGenomeDir\" -> \"A_map_repeats\" [label=\"genomeDir\"];\n  \"X_trim_umi\" -> \"A_map_repeats\" [label=\"readFilesIn\"];\n  \"A_map_repeats\" -> \"A_output_maprepeats_star_settings\";\n  \"A_map_genome\" -> \"A_output_mapgenome_star_settings\";\n  \"A_sort\" -> \"A_output_sorted_bam\";\n  \"step_fastqc_trim\" -> \"X_output_trim_first_fastqc_report\";\n  \"step_gzip_sort_repunmapped_fastq\" -> \"A_output_sort_repunmapped_fastq\";\n  \"A_map_repeats\" -> \"A_output_maprepeats_stats\";\n  \"step_gzip_sort_X_trim_again\" -> \"X_output_trim_again\";\n  \"A_map_genome\" -> \"A_output_mapgenome_stats\";\n  \"step_fastqc_trim\" -> \"X_output_trim_first_fastqc_stats\";\n  \"step_fastqc_trim_again\" -> \"X_output_trim_again_fastqc_stats\";\n  \"step_fastqc_trim_again\" -> \"X_output_trim_again_fastqc_report\";\n  \"X_trim_again\" -> \"X_output_trim_again_metrics\";\n  \"X_barcodecollapsese\" -> \"X_output_barcodecollapsese_bam\";\n  \"X_barcodecollapsese\" -> \"X_output_barcodecollapsese_metrics\";\n  \"X_trim\" -> \"X_output_trim_first_metrics\";\n  \"index_rmdup_bam\" -> \"X_output_sorted_bam\";\n  \"step_gzip_sort_X_trim\" -> \"X_output_trim_first\";\n  \"rename_mapped_genome\" -> \"A_output_mapgenome_mapped_to_genome\";\n  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