{"@id":"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl","retrievedFrom":{"repoUrl":"https://github.com/barski-lab/workflows.git","branch":"f2aee86fecd321efc6857b124350f079238ea2ba","path":"subworkflows/allele-vcf-alignreads-se-pe.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/barski-lab/workflows/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl","url":"https://github.com/barski-lab/workflows/blob/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl"},"retrievedOn":"2026-09-03T15:53:43.140+00:00","lastCommit":"f2aee86fecd321efc6857b124350f079238ea2ba","label":"allele-vcf-alignreads-se-pe.cwl","doc":"Workflow maps FASTQ files from `fastq_files` input into reference genome `reference_star_indices_folder` and\ninsilico generated `insilico_star_indices_folder` genome (concatenated genome for both `strain1` and `strain2` strains).\nFor both genomes STAR is run with `outFilterMultimapNmax` parameter set to 1 to discard all of the multimapped reads.\nFor insilico genome SAM file is generated. Then it's splitted into two SAM files based on strain names and then sorted\nby coordinates into the BAM format. For reference genome output BAM file from STAR slignment is also coordinate sorted.\n","inputs":{"strain1":{"label":"I strain name","doc":"First strain name","type":"String"},"strain2":{"label":"II strain name","doc":"Second strain name","type":"String"},"threads":{"label":"Number of threads","doc":"Number of threads for those steps that support multithreading","type":"Integer (Optional)"},"fastq_files":{"label":"Input FASTQ file(s)","doc":"Input FASTQ file or array of files","type":"File[]"},"strain1_chain_file":{"label":"I strain chain file","doc":"Chain file to project strain I to reference genome","type":"File"},"strain2_chain_file":{"label":"II strain chain file","doc":"Chain file to project strain II to reference genome","type":"File"},"reference_chrom_length_file":{"label":"Chromosome length file for reference genome","doc":"Chromosome length file for reference genome","type":"File"},"insilico_star_indices_folder":{"label":"STAR indices folder for insilico genome","doc":"Path to STAR generated indices folder for insilico genome","type":"Directory"},"reference_star_indices_folder":{"label":"STAR indices folder for reference genome","doc":"Path to STAR generated indices folder for reference genome","type":"Directory"}},"outputs":{"strain1_bigwig":{"label":"I strain bigWig file","doc":"Generated bigWig file for the first strain, projected to reference genome","type":"File"},"strain2_bigwig":{"label":"II strain bigWig file","doc":"Generated bigWig file for the second strain, projected to reference genome","type":"File"},"reference_bigwig":{"label":"Reference bigWig file","doc":"Generated BigWig file for the reference genome","type":"File"},"strain1_bambai_pair":{"label":"I strain output BAM","doc":"Coordinate sorted BAM file mapped to the first strain genome, projected to reference genome","type":"File"},"strain2_bambai_pair":{"label":"II strain output BAM","doc":"Coordinate sorted BAM file mapped to the second strain genome, projected to reference genome","type":"File"},"insilico_star_out_log":{"label":"STAR log out for insilico genome","doc":"STAR Log.out for insilico genome","type":"File (Optional)"},"reference_bambai_pair":{"label":"Reference output BAM","doc":"Coordinate sorted BAM file mapped to reference genome","type":"File"},"reference_star_out_log":{"label":"STAR log out for reference genome","doc":"STAR Log.out for reference genome","type":"File (Optional)"},"insilico_star_final_log":{"label":"STAR final log for insilico genome","doc":"STAR Log.final.out for insilico genome","type":"File"},"insilico_star_stdout_log":{"label":"STAR stdout log for insilico genome","doc":"STAR Log.std.out for insilico genome","type":"File (Optional)"},"reference_star_final_log":{"label":"STAR final log for reference genome","doc":"STAR Log.final.out for reference genome","type":"File"},"reference_star_stdout_log":{"label":"STAR stdout log for reference genome","doc":"STAR Log.std.out for reference genome","type":"File (Optional)"},"insilico_star_progress_log":{"label":"STAR progress log for insilico genome","doc":"STAR Log.progress.out for insilico genome","type":"File (Optional)"},"reference_star_progress_log":{"label":"STAR progress log for reference genome","doc":"STAR Log.progress.out for reference genome","type":"File (Optional)"}},"steps":{"strain1_project":{"doc":"Runs CrossMap.py script to project input BAM, BED, BIGWIG file based on input chain file.\nNot supported input file types: SAM, GFF, VCF, WIG\n\nIf `output_basename` is not set, call get_output_filename() and get_log_filename() functions to\nget default output and log filenames. Input `output_basename` should not include extension.\n","run":"../tools/crossmap.cwl","runType":"COMMANDLINETOOL","sources":{"strain1_project":{"sourceIDs":["strain1_chain_file"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#strain1_project/input_file":{"sourceIDs":["strain1_samtools_sort_index"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#strain1_project/input_file_type":{"defaultVal":"\\\"bam\\\""}}},"strain2_project":{"doc":"Runs CrossMap.py script to project input BAM, BED, BIGWIG file based on input chain file.\nNot supported input file types: SAM, GFF, VCF, WIG\n\nIf `output_basename` is not set, call get_output_filename() and get_log_filename() functions to\nget default output and log filenames. Input `output_basename` should not include extension.\n","run":"../tools/crossmap.cwl","runType":"COMMANDLINETOOL","sources":{"strain2_project":{"sourceIDs":["strain2_chain_file"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#strain2_project/input_file":{"sourceIDs":["strain2_samtools_sort_index"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#strain2_project/input_file_type":{"defaultVal":"\\\"bam\\\""}}},"strain1_sam_filter":{"doc":"Tool to run custom script set as `script` input with arguments from `param`.\nDefault script runs sed command over the input file and exports results to the file with the same name as input's basename\n","run":"../tools/custom-bash.cwl","runType":"COMMANDLINETOOL","sources":{"strain1_sam_filter":{"sourceIDs":["insilico_star_aligner"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#strain1_sam_filter/param":{"sourceIDs":["strain1"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#strain1_sam_filter/script":{"defaultVal":"\\\"cat \\\"$0\\\" | grep \\\"$1\\\" | sed \\\"s/$1/chr/g\\\"  > `basename $0`\\\""}}},"strain2_sam_filter":{"doc":"Tool to run custom script set as `script` input with arguments from `param`.\nDefault script runs sed command over the input file and exports results to the file with the same name as input's basename\n","run":"../tools/custom-bash.cwl","runType":"COMMANDLINETOOL","sources":{"strain2_sam_filter":{"defaultVal":"\\\"cat \\\"$0\\\" | grep \\\"$1\\\" | sed \\\"s/$1/chr/g\\\"  > `basename $0`\\\""},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#strain2_sam_filter/param":{"sourceIDs":["strain2"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#strain2_sam_filter/input_file":{"sourceIDs":["insilico_star_aligner"]}}},"insilico_star_aligner":{"doc":"Tool runs STAR alignReads.\n\n`default_output_name_prefix` function returns output files prefix if `outFileNamePrefix` is not set. By default prefix\nis equal to basename of `readFilesIn`.\n","run":"../tools/star-alignreads.cwl","runType":"COMMANDLINETOOL","sources":{"insilico_star_aligner":{"defaultVal":"\\\"SAM\\\""},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#insilico_star_aligner/threads":{"sourceIDs":["threads"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#insilico_star_aligner/genomeDir":{"sourceIDs":["insilico_star_indices_folder"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#insilico_star_aligner/readFilesIn":{"sourceIDs":["fastq_files"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#insilico_star_aligner/outFileNamePrefix":{"sourceIDs":["strain1"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#insilico_star_aligner/outFilterMultimapNmax":{"defaultVal":"1"}}},"strain1_bam_to_bigwig":{"doc":"Workflow converts input BAM file into bigWig and bedGraph files\n","run":"bam-bedgraph-bigwig.cwl","runType":"WORKFLOW","sources":{"strain1_bam_to_bigwig":{"sourceIDs":["insilico_star_aligner"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#strain1_bam_to_bigwig/bam_file":{"sourceIDs":["strain1_project"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#strain1_bam_to_bigwig/chrom_length_file":{"sourceIDs":["reference_chrom_length_file"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#strain1_bam_to_bigwig/mapped_reads_number":{"sourceIDs":["fastq_files"]}}},"strain2_bam_to_bigwig":{"doc":"Workflow converts input BAM file into bigWig and bedGraph files\n","run":"bam-bedgraph-bigwig.cwl","runType":"WORKFLOW","sources":{"strain2_bam_to_bigwig":{"sourceIDs":["insilico_star_aligner"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#strain2_bam_to_bigwig/bam_file":{"sourceIDs":["strain2_project"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#strain2_bam_to_bigwig/chrom_length_file":{"sourceIDs":["reference_chrom_length_file"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#strain2_bam_to_bigwig/mapped_reads_number":{"sourceIDs":["fastq_files"]}}},"reference_star_aligner":{"doc":"Tool runs STAR alignReads.\n\n`default_output_name_prefix` function returns output files prefix if `outFileNamePrefix` is not set. By default prefix\nis equal to basename of `readFilesIn`.\n","run":"../tools/star-alignreads.cwl","runType":"COMMANDLINETOOL","sources":{"reference_star_aligner":{"sourceIDs":["threads"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#reference_star_aligner/genomeDir":{"sourceIDs":["reference_star_indices_folder"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#reference_star_aligner/readFilesIn":{"sourceIDs":["fastq_files"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#reference_star_aligner/outFilterMultimapNmax":{"defaultVal":"1"}}},"reference_bam_to_bigwig":{"doc":"Workflow converts input BAM file into bigWig and bedGraph files\n","run":"bam-bedgraph-bigwig.cwl","runType":"WORKFLOW","sources":{"reference_bam_to_bigwig":{"sourceIDs":["reference_samtools_sort"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#reference_bam_to_bigwig/chrom_length_file":{"sourceIDs":["reference_chrom_length_file"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#reference_bam_to_bigwig/mapped_reads_number":{"sourceIDs":["fastq_files"]}}},"reference_samtools_sort":{"doc":"Tool to sort BAM/SAM file (set as input `sort_input`).\nIf input `trigger` is set to `true` or isn't set at all (`true` is used by default), run `samtools sort`, return\nnewly generated sorted BAM/SAM/CRAM file (the actual format of the output file depends on `out_format` value and\nextension of a filename set in `sort_output_filename`).\nIf input `trigger` is set to `false`, return unchanged BAM/SAM file, previously staged into output directory.\n\nBefore `baseCommand` is executed, input BAM/SAM file is staged into output directory (docker parameter `--workdir`),\nusing `InitialWorkDirRequirement`. Setting `writable: true` makes cwl-runner to copy input BAM/SAM file and\nmount it to docker container with `rw` mode as part of `--workdir` (if set to false, the file staged into output\ndirectory will be mounted to docker container separately with `ro` mode). Because `samtools sort` can overwrite input\nBAM/SAM file and save output with the same name, we don't need to rename it (as we did for samtools rmdup).\n\nTrigger logic is implemented in bash script set by default in input `bash_script`. If first argment $0 (which is `trigger` input)\nis true, run `samtools sort` with the rest of the arguments. If $0 is not true, skip `samtools sort` and return\ninput BAM/SAM file, previously staged into output directory.\n\nInput `trigger` is Boolean, but returns String, because of `valueFrom` field. The `valueFrom` is used, because if `trigger`\nis false, cwl-runner doesn't append this argument at all to the the `baseCommand` - new feature of CWL v1.0.2. Alternatively,\n`prefix` field could be used, but it causes changing logic in bash script saved in `bash_script` input.\n\n`default_output_name` function is used for generating output filename if input `sort_output_filename` is not set or in\ncase when `trigger` is false and we need to return original BAM/SAM file staged into output directory.\n\n`ext` function returns output filename extension on the base of `out_format` value. If input `out_format` is not set,\nuse `.bam` by default. If input `trigger` is false, `out_format` is ignored.\n\nIf `trigger` is set to true (or true is used by default), but both `sort_output_filename` and `out_format` are not set,\nthe output file format will be BAM by default.\n\nIf `trigger` is set to true (or true is used by default) and `sort_output_filename` is set to some value, but `out_format`\nis not set, the actual format of output file will be defined on the filename extension set in `sort_output_filename`\n(if filename doesn't have any extension, BAM is used by default). When `out_format` is also set, it overwrites extension\ngenerated on the base of `sort_output_filename` value.\n","run":"../tools/samtools-sort.cwl","runType":"COMMANDLINETOOL","sources":{"reference_samtools_sort":{"sourceIDs":["threads"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#reference_samtools_sort/sort_input":{"sourceIDs":["reference_star_aligner"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#reference_samtools_sort/sort_output_filename":{"sourceIDs":["fastq_files"]}}},"strain1_samtools_sort_index":{"doc":"Tool to sort and index input BAM/SAM/CRAM.\nIf input `trigger` is set to `true` or isn't set at all (`true` is used by default), run `samtools sort` and\n`samtools index`, return sorted BAM and BAI/CSI index file.\nIf input `trigger` is set to `false`, return unchanged `sort_input` (BAM/SAM/CRAM) and index (BAI/CSI, if provided in\n`secondaryFiles`) files, previously staged into output directory.\n\nBefore execution `baseCommand`, `sort_input` and `secondaryFiles` (if provided) are staged into directory\nset as docker parameter `--workdir` (tool's output directory), using `InitialWorkDirRequirement`. Setting\n`writable: true` makes cwl-runner to make copies of the `sort_input` and `secondaryFiles` (if provided) and mount\nthem to docker container with `rw` mode as part of `--workdir` (if set to false, the files staged into output\ndirectory will be mounted to docker container separately with `ro` mode). Because both `samtools sort` and\n`samtools index` can overwrite files with the same names (and in case of `samtools sort` even the input file can be\noverwritten), we don't need to rename any of the staged files.\n\nTrigger logic is implemented in two bash scripts set by default as `bash_script_sort` and `bash_script_index` inputs.\nFor both of then, if the first argument $0 (which is `trigger` input) is true, run `samtools sort/index` with the rest\nof the arguments. If $0 is not true, skip `samtools sort/index` and return `sort_input` and `secondaryFiles`\n(if provided) staged into output directory.\n\nInput `trigger` is Boolean, but returns String, because of `valueFrom` field. The `valueFrom` is used, because if `trigger`\nis false, cwl-runner doesn't append this argument at all to the the `baseCommand` - new feature of CWL v1.0.2. Alternatively,\n`prefix` field could be used, but it causes changing in script logic.\n\nIf using `sort_output_filename`, the output file extension should be `*.bam`, because `samtools sort` defines the output\nfile format on the base of the file extension. If `*.sam` is sed as output filename, it cannot be usefully indexed\nby `samtools index`.\n\n`default_bam` function is used to generate output filename for `samtools sort` if input `sort_output_filename` is not\nset or when `trigger` is false and we need to return `sort_input` and `secondaryFiles` (if provided) files staged into\noutput directory. Output filename is generated on the base of `sort_input` basename with `.bam` extension by default.\n\n`ext` function is used to return the index file extension (BAI/CSI) based on `csi` and `bai` inputs according to the\nfollowing logic\n  `csi` &&  `bai`  => BAI\n !`csi` && !`bai ` => BAI\n  `csi` && !`bai ` => CSI\n","run":"../tools/samtools-sort-index.cwl","runType":"COMMANDLINETOOL","sources":{"strain1_samtools_sort_index":{"sourceIDs":["threads"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#strain1_samtools_sort_index/sort_input":{"sourceIDs":["strain1_sam_filter"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#strain1_samtools_sort_index/sort_output_filename":{"sourceIDs":["strain1"]}}},"strain2_samtools_sort_index":{"doc":"Tool to sort and index input BAM/SAM/CRAM.\nIf input `trigger` is set to `true` or isn't set at all (`true` is used by default), run `samtools sort` and\n`samtools index`, return sorted BAM and BAI/CSI index file.\nIf input `trigger` is set to `false`, return unchanged `sort_input` (BAM/SAM/CRAM) and index (BAI/CSI, if provided in\n`secondaryFiles`) files, previously staged into output directory.\n\nBefore execution `baseCommand`, `sort_input` and `secondaryFiles` (if provided) are staged into directory\nset as docker parameter `--workdir` (tool's output directory), using `InitialWorkDirRequirement`. Setting\n`writable: true` makes cwl-runner to make copies of the `sort_input` and `secondaryFiles` (if provided) and mount\nthem to docker container with `rw` mode as part of `--workdir` (if set to false, the files staged into output\ndirectory will be mounted to docker container separately with `ro` mode). Because both `samtools sort` and\n`samtools index` can overwrite files with the same names (and in case of `samtools sort` even the input file can be\noverwritten), we don't need to rename any of the staged files.\n\nTrigger logic is implemented in two bash scripts set by default as `bash_script_sort` and `bash_script_index` inputs.\nFor both of then, if the first argument $0 (which is `trigger` input) is true, run `samtools sort/index` with the rest\nof the arguments. If $0 is not true, skip `samtools sort/index` and return `sort_input` and `secondaryFiles`\n(if provided) staged into output directory.\n\nInput `trigger` is Boolean, but returns String, because of `valueFrom` field. The `valueFrom` is used, because if `trigger`\nis false, cwl-runner doesn't append this argument at all to the the `baseCommand` - new feature of CWL v1.0.2. Alternatively,\n`prefix` field could be used, but it causes changing in script logic.\n\nIf using `sort_output_filename`, the output file extension should be `*.bam`, because `samtools sort` defines the output\nfile format on the base of the file extension. If `*.sam` is sed as output filename, it cannot be usefully indexed\nby `samtools index`.\n\n`default_bam` function is used to generate output filename for `samtools sort` if input `sort_output_filename` is not\nset or when `trigger` is false and we need to return `sort_input` and `secondaryFiles` (if provided) files staged into\noutput directory. Output filename is generated on the base of `sort_input` basename with `.bam` extension by default.\n\n`ext` function is used to return the index file extension (BAI/CSI) based on `csi` and `bai` inputs according to the\nfollowing logic\n  `csi` &&  `bai`  => BAI\n !`csi` && !`bai ` => BAI\n  `csi` && !`bai ` => CSI\n","run":"../tools/samtools-sort-index.cwl","runType":"COMMANDLINETOOL","sources":{"strain2_samtools_sort_index":{"sourceIDs":["threads"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#strain2_samtools_sort_index/sort_input":{"sourceIDs":["strain2_sam_filter"]},"https://w3id.org/cwl/view/git/f2aee86fecd321efc6857b124350f079238ea2ba/subworkflows/allele-vcf-alignreads-se-pe.cwl#strain2_samtools_sort_index/sort_output_filename":{"sourceIDs":["strain2"]}}}},"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    \"threads\" [fillcolor=\"#94DDF4\",label=\"Number of threads\"];\n    \"strain2_chain_file\" [fillcolor=\"#94DDF4\",label=\"II strain chain file\"];\n    \"strain1_chain_file\" [fillcolor=\"#94DDF4\",label=\"I strain chain file\"];\n    \"reference_star_indices_folder\" [fillcolor=\"#94DDF4\",label=\"STAR indices folder for reference genome\"];\n    \"fastq_files\" [fillcolor=\"#94DDF4\",label=\"Input FASTQ file(s)\"];\n    \"fastq_files\" [fillcolor=\"#94DDF4\",label=\"Input FASTQ file(s)\"];\n    \"strain2\" [fillcolor=\"#94DDF4\",label=\"II strain name\"];\n    \"strain1\" [fillcolor=\"#94DDF4\",label=\"I strain name\"];\n    \"insilico_star_indices_folder\" [fillcolor=\"#94DDF4\",label=\"STAR indices folder for insilico genome\"];\n    \"reference_chrom_length_file\" [fillcolor=\"#94DDF4\",label=\"Chromosome length file for reference genome\"];\n  }\n  subgraph cluster_outputs {\n    rank = \"same\";\n    style = \"dashed\";\n    labelloc = \"b\";\n    label = \"Workflow Outputs\";\n    \"strain2_bigwig\" [fillcolor=\"#94DDF4\",label=\"II strain bigWig file\"];\n    \"strain2_bambai_pair\" [fillcolor=\"#94DDF4\",label=\"II strain output BAM\"];\n    \"reference_bambai_pair\" [fillcolor=\"#94DDF4\",label=\"Reference output BAM\"];\n    \"reference_star_stdout_log\" [fillcolor=\"#94DDF4\",label=\"STAR stdout log for reference genome\"];\n    \"reference_star_final_log\" [fillcolor=\"#94DDF4\",label=\"STAR final log for reference genome\"];\n    \"strain1_bigwig\" [fillcolor=\"#94DDF4\",label=\"I strain bigWig file\"];\n    \"reference_star_out_log\" [fillcolor=\"#94DDF4\",label=\"STAR log out for reference genome\"];\n    \"insilico_star_out_log\" [fillcolor=\"#94DDF4\",label=\"STAR log out for insilico genome\"];\n    \"insilico_star_stdout_log\" [fillcolor=\"#94DDF4\",label=\"STAR stdout log for insilico genome\"];\n    \"reference_star_progress_log\" [fillcolor=\"#94DDF4\",label=\"STAR progress log for reference genome\"];\n    \"strain1_bambai_pair\" [fillcolor=\"#94DDF4\",label=\"I strain output BAM\"];\n    \"insilico_star_progress_log\" [fillcolor=\"#94DDF4\",label=\"STAR progress log for insilico genome\"];\n    \"insilico_star_final_log\" [fillcolor=\"#94DDF4\",label=\"STAR final log for insilico genome\"];\n    \"reference_bigwig\" [fillcolor=\"#94DDF4\",label=\"Reference bigWig file\"];\n  }\n  \"reference_star_aligner\" [label=\"reference_star_aligner\"];\n  \"insilico_star_aligner\" [label=\"insilico_star_aligner\"];\n  \"strain1_sam_filter\" [label=\"strain1_sam_filter\"];\n  \"strain1_project\" [label=\"strain1_project\"];\n  \"reference_samtools_sort\" [label=\"reference_samtools_sort\"];\n  \"strain1_samtools_sort_index\" [label=\"strain1_samtools_sort_index\"];\n  \"strain2_bam_to_bigwig\" [label=\"strain2_bam_to_bigwig\", fillcolor=\"#F3CEA1\"];\n  \"reference_bam_to_bigwig\" [label=\"reference_bam_to_bigwig\", fillcolor=\"#F3CEA1\"];\n  \"strain2_sam_filter\" [label=\"strain2_sam_filter\"];\n  \"strain2_project\" [label=\"strain2_project\"];\n  \"strain1_bam_to_bigwig\" [label=\"strain1_bam_to_bigwig\", fillcolor=\"#F3CEA1\"];\n  \"strain2_samtools_sort_index\" [label=\"strain2_samtools_sort_index\"];\n  \"threads\" -> \"reference_star_aligner\" [label=\"threads\"];\n  \"reference_star_indices_folder\" -> \"reference_star_aligner\" [label=\"genomeDir\"];\n  \"fastq_files\" -> \"reference_star_aligner\" [label=\"readFilesIn\"];\n  \"default1\" -> \"reference_star_aligner\" [label=\"outFilterMultimapNmax\"];\n  \"default1\" [label=\"1\", fillcolor=\"#D5AEFC\"];\n  \"default2\" -> \"insilico_star_aligner\" [label=\"outSAMtype\"];\n  \"default2\" [label=\"\\\"SAM\\\"\", fillcolor=\"#D5AEFC\"];\n  \"insilico_star_indices_folder\" -> \"insilico_star_aligner\" [label=\"genomeDir\"];\n  \"fastq_files\" -> \"insilico_star_aligner\" [label=\"readFilesIn\"];\n  \"threads\" -> \"insilico_star_aligner\" [label=\"threads\"];\n  \"default3\" -> \"insilico_star_aligner\" [label=\"outFilterMultimapNmax\"];\n  \"default3\" [label=\"1\", fillcolor=\"#D5AEFC\"];\n  \"strain2\" -> \"insilico_star_aligner\" [label=\"outFileNamePrefix\"];\n  \"strain1\" -> \"insilico_star_aligner\" [label=\"outFileNamePrefix\"];\n  \"insilico_star_aligner\" -> \"strain1_sam_filter\" [label=\"input_file\"];\n  \"default4\" -> \"strain1_sam_filter\" [label=\"script\"];\n  \"default4\" [label=\"\\\"cat \\\"$0\\\" | grep \\\"$1\\\" | sed \\\"s/$1/chr/g\\\"  > `basename $0`\\\"\", fillcolor=\"#D5AEFC\"];\n  \"strain1\" -> \"strain1_sam_filter\" [label=\"param\"];\n  \"strain1_chain_file\" -> \"strain1_project\" [label=\"chain_file\"];\n  \"default5\" -> \"strain1_project\" [label=\"input_file_type\"];\n  \"default5\" [label=\"\\\"bam\\\"\", fillcolor=\"#D5AEFC\"];\n  \"strain1_samtools_sort_index\" -> \"strain1_project\" [label=\"input_file\"];\n  \"threads\" -> \"reference_samtools_sort\" [label=\"threads\"];\n  \"fastq_files\" -> \"reference_samtools_sort\" [label=\"sort_output_filename\"];\n  \"reference_star_aligner\" -> \"reference_samtools_sort\" [label=\"sort_input\"];\n  \"threads\" -> \"strain1_samtools_sort_index\" [label=\"threads\"];\n  \"strain1_sam_filter\" -> \"strain1_samtools_sort_index\" [label=\"sort_input\"];\n  \"fastq_files\" -> \"strain1_samtools_sort_index\" [label=\"sort_output_filename\"];\n  \"strain1\" -> \"strain1_samtools_sort_index\" [label=\"sort_output_filename\"];\n  \"insilico_star_aligner\" -> \"strain2_bam_to_bigwig\" [label=\"mapped_reads_number\"];\n  \"fastq_files\" -> \"strain2_bam_to_bigwig\" [label=\"mapped_reads_number\"];\n  \"reference_chrom_length_file\" -> \"strain2_bam_to_bigwig\" [label=\"chrom_length_file\"];\n  \"strain2_project\" -> \"strain2_bam_to_bigwig\" [label=\"bam_file\"];\n  \"reference_samtools_sort\" -> \"reference_bam_to_bigwig\" [label=\"bam_file\"];\n  \"reference_chrom_length_file\" -> \"reference_bam_to_bigwig\" [label=\"chrom_length_file\"];\n  \"reference_star_aligner\" -> \"reference_bam_to_bigwig\" [label=\"mapped_reads_number\"];\n  \"fastq_files\" -> \"reference_bam_to_bigwig\" [label=\"mapped_reads_number\"];\n  \"default6\" -> \"strain2_sam_filter\" [label=\"script\"];\n  \"default6\" [label=\"\\\"cat \\\"$0\\\" | grep \\\"$1\\\" | sed \\\"s/$1/chr/g\\\"  > `basename $0`\\\"\", fillcolor=\"#D5AEFC\"];\n  \"strain2\" -> \"strain2_sam_filter\" [label=\"param\"];\n  \"insilico_star_aligner\" -> \"strain2_sam_filter\" [label=\"input_file\"];\n  \"strain2_chain_file\" -> \"strain2_project\" [label=\"chain_file\"];\n  \"default7\" -> \"strain2_project\" [label=\"input_file_type\"];\n  \"default7\" [label=\"\\\"bam\\\"\", fillcolor=\"#D5AEFC\"];\n  \"strain2_samtools_sort_index\" -> \"strain2_project\" [label=\"input_file\"];\n  \"insilico_star_aligner\" -> \"strain1_bam_to_bigwig\" [label=\"mapped_reads_number\"];\n  \"fastq_files\" -> \"strain1_bam_to_bigwig\" [label=\"mapped_reads_number\"];\n  \"reference_chrom_length_file\" -> \"strain1_bam_to_bigwig\" [label=\"chrom_length_file\"];\n  \"strain1_project\" -> \"strain1_bam_to_bigwig\" [label=\"bam_file\"];\n  \"threads\" -> \"strain2_samtools_sort_index\" [label=\"threads\"];\n  \"strain2_sam_filter\" -> \"strain2_samtools_sort_index\" [label=\"sort_input\"];\n  \"fastq_files\" -> \"strain2_samtools_sort_index\" [label=\"sort_output_filename\"];\n  \"strain2\" -> \"strain2_samtools_sort_index\" [label=\"sort_output_filename\"];\n  \"strain2_bam_to_bigwig\" -> \"strain2_bigwig\";\n  \"strain2_project\" -> \"strain2_bambai_pair\";\n  \"reference_samtools_sort\" -> \"reference_bambai_pair\";\n  \"reference_star_aligner\" -> \"reference_star_stdout_log\";\n  \"reference_star_aligner\" -> \"reference_star_final_log\";\n  \"strain1_bam_to_bigwig\" -> \"strain1_bigwig\";\n  \"reference_star_aligner\" -> \"reference_star_out_log\";\n  \"insilico_star_aligner\" -> \"insilico_star_out_log\";\n  \"insilico_star_aligner\" -> \"insilico_star_stdout_log\";\n  \"reference_star_aligner\" -> \"reference_star_progress_log\";\n  \"strain1_project\" -> \"strain1_bambai_pair\";\n  \"insilico_star_aligner\" -> \"insilico_star_progress_log\";\n  \"insilico_star_aligner\" -> \"insilico_star_final_log\";\n  \"reference_bam_to_bigwig\" -> 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