{"@id":"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl","retrievedFrom":{"repoUrl":"https://github.com/datirium/workflows.git","branch":"d1bef74924efcb8bfaa00987b3f148d5a192b7a9","path":"workflows/genome-indices.cwl","packedId":null,"type":"GITHUB","rawUrl":"https://raw.githubusercontent.com/datirium/workflows/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl","url":"https://github.com/datirium/workflows/blob/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl"},"retrievedOn":"2025-01-27T04:00:54.756+00:00","lastCommit":"d1bef74924efcb8bfaa00987b3f148d5a192b7a9","label":"Generate genome indices for STAR & bowtie","doc":"Creates indices for:\n * [STAR](https://github.com/alexdobin/STAR) v2.5.3a (03/17/2017) PMID: [23104886](https://www.ncbi.nlm.nih.gov/pubmed/23104886)\n * [bowtie](http://bowtie-bio.sourceforge.net/tutorial.shtml) v1.2.0 (12/30/2016)\n\nIt performs the following steps:\n\n1. `STAR --runMode genomeGenerate` to generate indices, based on [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) and [GTF](http://mblab.wustl.edu/GTF2.html) input files, returns results as an array of files\n2. Outputs indices as [Direcotry](http://www.commonwl.org/v1.0/CommandLineTool.html#Directory) data type\n3. Separates *chrNameLength.txt* file from Directory output\n4. `bowtie-build` to generate indices requires genome [FASTA](http://zhanglab.ccmb.med.umich.edu/FASTA/) file as input, returns results as a group of main and secondary files","inputs":{"genome":{"label":"Genome type","doc":"Genome type, such as mm10, hg19, hg38, etc","type":"String"},"threads":{"label":"Number of threads to run tools","doc":"Number of threads for those steps that support multithreading","type":"Integer (Optional)"},"cytoband":{"label":"Compressed cytoBand file for IGV browser","doc":"Compressed tab-separated cytoBand file for IGV browser","type":"File [TSV]","format":"http://edamontology.org/format_3475"},"genome_file":{"label":"Reference genome file (*.2bit, *.fasta, *.fa, *.fa.gz, *.fasta.gz)","doc":"Reference genome file (*.2bit, *.fasta, *.fa, *.fa.gz, *.fasta.gz). All chromosomes are included","type":"File [2bit]","format":"http://edamontology.org/format_3009"},"genome_label":{"label":"Genome label","type":"String (Optional)"},"annotation_tab":{"label":"Compressed tsv.gz annotation file","doc":"Compressed tab-separated annotation file. Doesn't include chrM","type":"File [TSV]","format":"http://edamontology.org/format_3475"},"genome_details":{"label":"Genome details","type":"String (Optional)"},"chromosome_list":{"label":"Chromosome list to be included into the reference genome FASTA file","doc":"Filter chromosomes while extracting FASTA from 2bit","type":"String[] (Optional)"},"fasta_ribosomal":{"label":"Ribosomal DNA file (*.fasta, *.fa)","doc":"Ribosomal DNA file (*.fasta, *.fa). Default: hg19","type":"File (Optional) [FASTA]","format":"http://edamontology.org/format_1929"},"genome_description":{"label":"Genome description","type":"String (Optional)"},"genome_sa_sparse_d":{"label":"Suffix array sparsity for reference genome and mitochondrial DNA indices","doc":"Suffix array sparsity, i.e. distance between indices: use bigger\nnumbers to decrease needed RAMat the cost of mapping speed reduction\\\"\n","type":"Integer (Optional)"},"effective_genome_size":{"label":"Effective genome size","doc":"MACS2 effective genome sizes: hs, mm, ce, dm or number, for example 2.7e9","type":"String"},"genome_chr_bin_n_bits":{"label":"Number of bins allocated for each chromosome of reference genome","doc":"If you are using a genome with a large (>5,000) number of references (chrosomes/scaffolds), you may need to reduce the\n--genomeChrBinNbits to reduce RAM consumption. For a genome with large number of contigs, it is recommended to scale\nthis parameter as min(18, log2[max(GenomeLength/NumberOfReferences,ReadLength)]).\ndefault: 18\n","type":"Integer (Optional)"},"genome_sa_index_n_bases":{"label":"Length of SA pre-indexing string for reference genome indices","doc":"Length (bases) of the SA pre-indexing string. Typically between 10 and 15. Longer strings will use much more memory,\nbut allow faster searches. For small genomes, the parameter –genomeSAindexNbases must be scaled down to\nmin(14, log2(GenomeLength)/2 - 1). For example, for 1 megaBase genome, this is equal to 9, for 100 kiloBase genome,\nthis is equal to 7.\ndefault: 14\n","type":"Integer (Optional)"},"limit_genome_generate_ram":{"label":"Limit maximum available RAM (bytes) for reference genome indices generation","doc":"Maximum available RAM (bytes) for genome generation. Default 31000000000","type":"Long (Optional)"},"mitochondrial_annotation_tab":{"label":"Compressed tsv.gz mitochondrial DNA annotation file","doc":"Compressed mitochondrial DNA tab-separated annotation file. Includes only chrM","type":"File [TSV]","format":"http://edamontology.org/format_3475"},"genome_sa_index_n_bases_mitochondrial":{"label":"Length of SA pre-indexing string for mitochondrial DNA indices","doc":"Length (bases) of the SA pre-indexing string. Typically between 10 and 15. Longer strings will use much more memory,\nbut allow faster searches. For small genomes, the parameter –genomeSAindexNbases must be scaled down to\nmin(14, log2(GenomeLength)/2 - 1). For example, for 1 megaBase genome, this is equal to 9, for 100 kiloBase genome,\nthis is equal to 7.\ndefault: 14\n","type":"Integer (Optional)"}},"outputs":{"annotation":{"label":"TSV annotation file","doc":"Tab-separated annotation file. Includes reference genome and mitochondrial DNA annotations","type":"File [TSV]","format":"http://edamontology.org/format_3475"},"genome_size":{"label":"Effective genome size","doc":"MACS2 effective genome sizes: hs, mm, ce, dm or number, for example 2.7e9","type":"String"},"chrom_length":{"label":"Genome chromosome length file","doc":"Genome chromosome length file","type":"File [Textual format]","format":"http://edamontology.org/format_2330"},"fasta_output":{"label":"Reference genome FASTA file","doc":"Reference genome FASTA file. Includes only selected chromosomes","type":"File [FASTA]","format":"http://edamontology.org/format_1929"},"star_indices":{"label":"STAR genome indices","doc":"STAR generated genome indices folder","type":"Directory"},"annotation_bed":{"label":"Sorted BED annotation file","doc":"Sorted BED annotation file","type":"File [BED]","format":"http://edamontology.org/format_3003"},"annotation_gtf":{"label":"GTF annotation file","doc":"GTF annotation file. Includes reference genome and mitochondrial DNA annotations","type":"File [GTF]","format":"http://edamontology.org/format_2306"},"bowtie_indices":{"label":"Bowtie genome indices","doc":"Bowtie generated genome indices folder","type":"Directory"},"cytoband_output":{"label":"CytoBand file for IGV browser","doc":"Tab-separated cytoBand file for IGV browser","type":"File [TSV]","format":"http://edamontology.org/format_3475"},"fasta_fai_output":{"label":"FAI index for genome FASTA file","doc":"Tab-separated FAI index file","type":"File [TSV]","format":"http://edamontology.org/format_3475"},"ribosomal_indices":{"label":"Bowtie ribosomal DNA indices","doc":"Bowtie generated ribosomal DNA indices folder","type":"Directory"},"annotation_bed_tbi":{"label":"Sorted bigBed annotation file","doc":"Sorted bigBed annotation file","type":"File [bigBed]","format":"http://edamontology.org/format_3004"},"mitochondrial_indices":{"label":"STAR mitochondrial DNA indices","doc":"STAR generated mitochondrial DNA indices folder","type":"Directory"},"star_indices_stderr_log":{"label":"STAR stderr log for genome indices","doc":"STAR generated stderr log for genome indices","type":"File"},"star_indices_stdout_log":{"label":"STAR stdout log for genome indices","doc":"STAR generated stdout log for genome indices","type":"File"},"bowtie_indices_stderr_log":{"label":"Bowtie stderr log genome indices","doc":"Bowtie generated stderr log for genome indices","type":"File"},"bowtie_indices_stdout_log":{"label":"Bowtie stdout log for genome indices","doc":"Bowtie generated stdout log for genome indices","type":"File"},"ribosomal_indices_stderr_log":{"label":"Bowtie stderr log for ribosomal DNA indices","doc":"Bowtie generated stderr log for ribosomal DNA indices","type":"File"},"ribosomal_indices_stdout_log":{"label":"Bowtie stdout log for ribosomal DNA indices","doc":"Bowtie generated stdout log for ribosomal DNA indices","type":"File"},"mitochondrial_indices_stderr_log":{"label":"STAR stderr log for mitochondrial DNA indices","doc":"STAR generated stderr log for mitochondrial DNA indices","type":"File"},"mitochondrial_indices_stdout_log":{"label":"STAR stdout log for mitochondrial DNA indices","doc":"STAR generated stdout log for mitochondrial DNA indices","type":"File"}},"steps":{"index_fasta":{"doc":"Generates FAI index file for input FASTA file\nOutput file has the same basename, as input file, but with updated `.fai` extension. `samtools faidx` exports\noutput file alognside the input file. To prevent tool from failing, `input_file` should be staged into output\ndirectory using `\\\"writable\\\": true`. Setting `writable: true` makes cwl-runner to make a copy of input 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)\n","run":"../tools/samtools-faidx.cwl","runType":"COMMANDLINETOOL","sources":{"index_fasta":{"sourceIDs":["extract_fasta"]}}},"extract_fasta":{"doc":"twoBitToFa - Convert all or part of .2bit file to fasta.\nOutputs only those chromosomes that are set in chr_list intput.\nTool will fail if you include in chr_list those chromosomes that are absent in 2bit file.\nIf gz is provided - use gunzip instead of twoBitToFa\nIf FASTA file is provided, do nothing\n","run":"../tools/ucsc-twobit-to-fa.cwl","runType":"COMMANDLINETOOL","sources":{"extract_fasta":{"sourceIDs":["genome_file"]},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#extract_fasta/chr_list":{"sourceIDs":["chromosome_list"]}}},"extract_cytoband":{"run":"genome-indices.cwl#extract_cytoband/106ad12d-e0d8-4052-b6cb-2758876132d3","runType":"COMMANDLINETOOL","sources":{"extract_cytoband":{"sourceIDs":["cytoband"]}}},"prepare_annotation":{"run":"genome-indices.cwl#prepare_annotation/f3c8c7d9-5ec4-48be-addd-0b2f6314ed04","runType":"COMMANDLINETOOL","sources":{"prepare_annotation":{"sourceIDs":["annotation_tab"]},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#prepare_annotation/chromosome_list":{"sourceIDs":["chromosome_list"]},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#prepare_annotation/mitochondrial_annotation":{"sourceIDs":["mitochondrial_annotation_tab"]}}},"sort_annotation_bed":{"doc":"Tool sorts data from `unsorted_file` by key\n\n`default_output_filename` function returns file name identical to `unsorted_file`, if `output_filename` is not provided.\n","run":"../tools/linux-sort.cwl","runType":"COMMANDLINETOOL","sources":{"sort_annotation_bed":{"sourceIDs":["convert_annotation_to_bed"]},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#sort_annotation_bed/key":{"defaultVal":"\\\"1,1\\\""}}},"star_generate_indices":{"doc":"Tool returns directory with indices generated by STAR. If genome_dir input is not provided,\nuse default output directory name star_indices.\nOutput chr_name_length should not be moved outside the indices folder.\n","run":"../tools/star-genomegenerate.cwl","runType":"COMMANDLINETOOL","sources":{"star_generate_indices":{"sourceIDs":["prepare_annotation"]},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#star_generate_indices/threads":{"sourceIDs":["threads"]},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#star_generate_indices/genome_dir":{"sourceIDs":["genome"]},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#star_generate_indices/genome_fasta_files":{"sourceIDs":["extract_fasta"]},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#star_generate_indices/genome_sa_sparse_d":{"sourceIDs":["genome_sa_sparse_d"]},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#star_generate_indices/genome_chr_bin_n_bits":{"sourceIDs":["genome_chr_bin_n_bits"]},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#star_generate_indices/genome_sa_index_n_bases":{"sourceIDs":["genome_sa_index_n_bases"]},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#star_generate_indices/limit_genome_generate_ram":{"sourceIDs":["limit_genome_generate_ram"]}}},"bowtie_generate_indices":{"doc":"Tool runs bowtie-build\nNot supported parameters:\n -c - reference sequences given on cmd line (as )\n","run":"../tools/bowtie-build.cwl","runType":"COMMANDLINETOOL","sources":{"bowtie_generate_indices":{"sourceIDs":["extract_fasta"]},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#bowtie_generate_indices/index_base_name":{"sourceIDs":["genome"]}}},"annotation_bed_to_bigbed":{"doc":"Tool converts bed file to bigBed\n\nBefore running `baseCommand` the following files are created in Docker working directory (using\n`InitialWorkDirRequirement`):\n`narrowpeak.as` - default BED file structure template for ENCODE narrowPeak format\n`broadpeak.as` - default BED file structure template for ENCODE broadPeak format\n\n`default_output_filename` function returns default output file name based on `input_bed` basename with `*.bb`\nextension if `output_filename` is not provided.\n\n`get_bed_type` function returns default BED file type if `bed_type` is not provided. Depending on `input_bed` file\nextension the following values are returned:\n `*.narrowpeak` --> bed6+4\n `*.broadpeak` --> bed6+3\n else --> null (`bedToBigBed` will use its own default value)\n\n`get_bed_template` function returns default BED file template if `bed_template` is not provided. Depending on\n`input_bed` file extension the following values are returned:\n `*.narrowpeak` --> narrowpeak.as (previously staged into Docker working directory)\n `*.broadpeak` --> broadpeak.as (previously staged into Docker working directory)\n else --> null (`bedToBigBed` will use its own default value)\n","run":"../tools/ucsc-bedtobigbed.cwl","runType":"COMMANDLINETOOL","sources":{"annotation_bed_to_bigbed":{"sourceIDs":["sort_annotation_bed"]},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#annotation_bed_to_bigbed/bed_type":{"defaultVal":"\\\"bed4+8\\\""},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#annotation_bed_to_bigbed/input_bed":{"sourceIDs":["sort_annotation_bed"]},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#annotation_bed_to_bigbed/chrom_length_file":{"sourceIDs":["star_generate_indices"]}}},"convert_annotation_to_bed":{"run":"genome-indices.cwl#convert_annotation_to_bed/719f95f2-2c55-43e7-b57b-f202d45cbfdc","runType":"COMMANDLINETOOL","sources":{"convert_annotation_to_bed":{"sourceIDs":["prepare_annotation"]}}},"ribosomal_generate_indices":{"doc":"Tool runs bowtie-build\nNot supported parameters:\n -c - reference sequences given on cmd line (as )\n","run":"../tools/bowtie-build.cwl","runType":"COMMANDLINETOOL","sources":{"ribosomal_generate_indices":{"sourceIDs":["genome"]},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#ribosomal_generate_indices/fasta_file":{"sourceIDs":["fasta_ribosomal"]}}},"extract_mitochondrial_fasta":{"doc":"twoBitToFa - Convert all or part of .2bit file to fasta.\nOutputs only those chromosomes that are set in chr_list intput.\nTool will fail if you include in chr_list those chromosomes that are absent in 2bit file.\nIf gz is provided - use gunzip instead of twoBitToFa\nIf FASTA file is provided, do nothing\n","run":"../tools/ucsc-twobit-to-fa.cwl","runType":"COMMANDLINETOOL","sources":{"extract_mitochondrial_fasta":{"defaultVal":"\\\"chrM\\\""},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#extract_mitochondrial_fasta/reference_file":{"sourceIDs":["genome_file"]}}},"mitochondrial_generate_indices":{"doc":"Tool returns directory with indices generated by STAR. If genome_dir input is not provided,\nuse default output directory name star_indices.\nOutput chr_name_length should not be moved outside the indices folder.\n","run":"../tools/star-genomegenerate.cwl","runType":"COMMANDLINETOOL","sources":{"mitochondrial_generate_indices":{"sourceIDs":["threads"]},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#mitochondrial_generate_indices/genome_dir":{"sourceIDs":["genome"]},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#mitochondrial_generate_indices/sjdb_gtf_file":{"sourceIDs":["prepare_annotation"]},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#mitochondrial_generate_indices/genome_fasta_files":{"sourceIDs":["extract_mitochondrial_fasta"]},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#mitochondrial_generate_indices/genome_sa_sparse_d":{"sourceIDs":["genome_sa_sparse_d"]},"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl#mitochondrial_generate_indices/genome_sa_index_n_bases":{"sourceIDs":["genome_sa_index_n_bases_mitochondrial"]}}}},"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 \"genome_chr_bin_n_bits\" [fillcolor=\"#94DDF4\",label=\"Number of bins allocated for each chromosome of reference genome\"];\n \"threads\" [fillcolor=\"#94DDF4\",label=\"Number of threads to run tools\"];\n \"genome_sa_index_n_bases\" [fillcolor=\"#94DDF4\",label=\"Length of SA pre-indexing string for reference genome indices\"];\n \"genome\" [fillcolor=\"#94DDF4\",label=\"Genome type\"];\n \"effective_genome_size\" [fillcolor=\"#94DDF4\",label=\"Effective genome size\"];\n \"fasta_ribosomal\" [fillcolor=\"#94DDF4\",label=\"Ribosomal DNA file (*.fasta, *.fa)\"];\n \"genome_file\" [fillcolor=\"#94DDF4\",label=\"Reference genome file (*.2bit, *.fasta, *.fa, *.fa.gz, *.fasta.gz)\"];\n \"limit_genome_generate_ram\" [fillcolor=\"#94DDF4\",label=\"Limit maximum available RAM (bytes) for reference genome indices generation\"];\n \"genome_details\" [fillcolor=\"#94DDF4\",label=\"Genome details\"];\n \"annotation_tab\" [fillcolor=\"#94DDF4\",label=\"Compressed tsv.gz annotation file\"];\n \"mitochondrial_annotation_tab\" [fillcolor=\"#94DDF4\",label=\"Compressed tsv.gz mitochondrial DNA annotation file\"];\n \"chromosome_list\" [fillcolor=\"#94DDF4\",label=\"Chromosome list to be included into the reference genome FASTA file\"];\n \"genome_sa_sparse_d\" [fillcolor=\"#94DDF4\",label=\"Suffix array sparsity for reference genome and mitochondrial DNA indices\"];\n \"genome_sa_index_n_bases_mitochondrial\" [fillcolor=\"#94DDF4\",label=\"Length of SA pre-indexing string for mitochondrial DNA indices\"];\n \"cytoband\" [fillcolor=\"#94DDF4\",label=\"Compressed cytoBand file for IGV browser\"];\n \"genome_description\" [fillcolor=\"#94DDF4\",label=\"Genome description\"];\n \"genome_label\" [fillcolor=\"#94DDF4\",label=\"Genome label\"];\n }\n subgraph cluster_outputs {\n rank = \"same\";\n style = \"dashed\";\n labelloc = \"b\";\n label = \"Workflow Outputs\";\n \"fasta_output\" [fillcolor=\"#94DDF4\",label=\"Reference genome FASTA file\"];\n \"star_indices\" [fillcolor=\"#94DDF4\",label=\"STAR genome indices\"];\n \"bowtie_indices_stderr_log\" [fillcolor=\"#94DDF4\",label=\"Bowtie stderr log genome indices\"];\n \"mitochondrial_indices\" [fillcolor=\"#94DDF4\",label=\"STAR mitochondrial DNA indices\"];\n \"mitochondrial_indices_stdout_log\" [fillcolor=\"#94DDF4\",label=\"STAR stdout log for mitochondrial DNA indices\"];\n \"ribosomal_indices\" [fillcolor=\"#94DDF4\",label=\"Bowtie ribosomal DNA indices\"];\n \"genome_size\" [fillcolor=\"#94DDF4\",label=\"Effective genome size\"];\n \"bowtie_indices\" [fillcolor=\"#94DDF4\",label=\"Bowtie genome indices\"];\n \"mitochondrial_indices_stderr_log\" [fillcolor=\"#94DDF4\",label=\"STAR stderr log for mitochondrial DNA indices\"];\n \"chrom_length\" [fillcolor=\"#94DDF4\",label=\"Genome chromosome length file\"];\n \"star_indices_stdout_log\" [fillcolor=\"#94DDF4\",label=\"STAR stdout log for genome indices\"];\n \"annotation_bed\" [fillcolor=\"#94DDF4\",label=\"Sorted BED annotation file\"];\n \"bowtie_indices_stdout_log\" [fillcolor=\"#94DDF4\",label=\"Bowtie stdout log for genome indices\"];\n \"ribosomal_indices_stdout_log\" [fillcolor=\"#94DDF4\",label=\"Bowtie stdout log for ribosomal DNA indices\"];\n \"annotation\" [fillcolor=\"#94DDF4\",label=\"TSV annotation file\"];\n \"star_indices_stderr_log\" [fillcolor=\"#94DDF4\",label=\"STAR stderr log for genome indices\"];\n \"annotation_bed_tbi\" [fillcolor=\"#94DDF4\",label=\"Sorted bigBed annotation file\"];\n \"annotation_gtf\" [fillcolor=\"#94DDF4\",label=\"GTF annotation file\"];\n \"fasta_fai_output\" [fillcolor=\"#94DDF4\",label=\"FAI index for genome FASTA file\"];\n \"ribosomal_indices_stderr_log\" [fillcolor=\"#94DDF4\",label=\"Bowtie stderr log for ribosomal DNA indices\"];\n \"cytoband_output\" [fillcolor=\"#94DDF4\",label=\"CytoBand file for IGV browser\"];\n }\n \"ribosomal_generate_indices\" [label=\"ribosomal_generate_indices\"];\n \"mitochondrial_generate_indices\" [label=\"mitochondrial_generate_indices\"];\n \"extract_fasta\" [label=\"extract_fasta\"];\n \"star_generate_indices\" [label=\"star_generate_indices\"];\n \"sort_annotation_bed\" [label=\"sort_annotation_bed\"];\n \"prepare_annotation\" [label=\"prepare_annotation\"];\n \"annotation_bed_to_bigbed\" [label=\"annotation_bed_to_bigbed\"];\n \"convert_annotation_to_bed\" [label=\"convert_annotation_to_bed\"];\n \"extract_cytoband\" [label=\"extract_cytoband\"];\n \"extract_mitochondrial_fasta\" [label=\"extract_mitochondrial_fasta\"];\n \"index_fasta\" [label=\"index_fasta\"];\n \"bowtie_generate_indices\" [label=\"bowtie_generate_indices\"];\n \"genome\" -> \"ribosomal_generate_indices\" [label=\"index_base_name\"];\n \"fasta_ribosomal\" -> \"ribosomal_generate_indices\" [label=\"fasta_file\"];\n \"threads\" -> \"mitochondrial_generate_indices\" [label=\"threads\"];\n \"genome_sa_sparse_d\" -> \"mitochondrial_generate_indices\" [label=\"genome_sa_sparse_d\"];\n \"extract_mitochondrial_fasta\" -> \"mitochondrial_generate_indices\" [label=\"genome_fasta_files\"];\n \"prepare_annotation\" -> \"mitochondrial_generate_indices\" [label=\"sjdb_gtf_file\"];\n \"genome_sa_index_n_bases_mitochondrial\" -> \"mitochondrial_generate_indices\" [label=\"genome_sa_index_n_bases\"];\n \"genome\" -> \"mitochondrial_generate_indices\" [label=\"genome_dir\"];\n \"genome_file\" -> \"extract_fasta\" [label=\"reference_file\"];\n \"chromosome_list\" -> \"extract_fasta\" [label=\"chr_list\"];\n \"prepare_annotation\" -> \"star_generate_indices\" [label=\"sjdb_gtf_file\"];\n \"genome_chr_bin_n_bits\" -> \"star_generate_indices\" [label=\"genome_chr_bin_n_bits\"];\n \"genome_sa_index_n_bases\" -> \"star_generate_indices\" [label=\"genome_sa_index_n_bases\"];\n \"genome\" -> \"star_generate_indices\" [label=\"genome_dir\"];\n \"extract_fasta\" -> \"star_generate_indices\" [label=\"genome_fasta_files\"];\n \"genome_sa_sparse_d\" -> \"star_generate_indices\" [label=\"genome_sa_sparse_d\"];\n \"limit_genome_generate_ram\" -> \"star_generate_indices\" [label=\"limit_genome_generate_ram\"];\n \"threads\" -> \"star_generate_indices\" [label=\"threads\"];\n \"convert_annotation_to_bed\" -> \"sort_annotation_bed\" [label=\"unsorted_file\"];\n \"default1\" -> \"sort_annotation_bed\" [label=\"key\"];\n \"default1\" [label=\"\\\"2,2n\\\"\", fillcolor=\"#D5AEFC\"];\n \"default2\" -> \"sort_annotation_bed\" [label=\"key\"];\n \"default2\" [label=\"\\\"1,1\\\"\", fillcolor=\"#D5AEFC\"];\n \"annotation_tab\" -> \"prepare_annotation\" [label=\"genome_annotation\"];\n \"mitochondrial_annotation_tab\" -> \"prepare_annotation\" [label=\"mitochondrial_annotation\"];\n \"chromosome_list\" -> \"prepare_annotation\" [label=\"chromosome_list\"];\n \"sort_annotation_bed\" -> \"annotation_bed_to_bigbed\" [label=\"output_filename\"];\n \"default3\" -> \"annotation_bed_to_bigbed\" [label=\"bed_type\"];\n \"default3\" [label=\"\\\"bed4+8\\\"\", fillcolor=\"#D5AEFC\"];\n \"star_generate_indices\" -> \"annotation_bed_to_bigbed\" [label=\"chrom_length_file\"];\n \"sort_annotation_bed\" -> \"annotation_bed_to_bigbed\" [label=\"input_bed\"];\n \"prepare_annotation\" -> \"convert_annotation_to_bed\" [label=\"annotation_tsv_file\"];\n \"cytoband\" -> \"extract_cytoband\" [label=\"input_file\"];\n \"default4\" -> \"extract_mitochondrial_fasta\" [label=\"chr_list\"];\n \"default4\" [label=\"\\\"chrM\\\"\", fillcolor=\"#D5AEFC\"];\n \"genome_file\" -> \"extract_mitochondrial_fasta\" [label=\"reference_file\"];\n \"extract_fasta\" -> \"index_fasta\" [label=\"fasta_file\"];\n \"extract_fasta\" -> \"bowtie_generate_indices\" [label=\"fasta_file\"];\n \"genome\" -> \"bowtie_generate_indices\" [label=\"index_base_name\"];\n \"extract_fasta\" -> \"fasta_output\";\n \"star_generate_indices\" -> \"star_indices\";\n \"bowtie_generate_indices\" -> \"bowtie_indices_stderr_log\";\n \"mitochondrial_generate_indices\" -> \"mitochondrial_indices\";\n \"mitochondrial_generate_indices\" -> \"mitochondrial_indices_stdout_log\";\n \"ribosomal_generate_indices\" -> \"ribosomal_indices\";\n \"effective_genome_size\" -> \"genome_size\";\n \"bowtie_generate_indices\" -> \"bowtie_indices\";\n \"mitochondrial_generate_indices\" -> \"mitochondrial_indices_stderr_log\";\n \"star_generate_indices\" -> \"chrom_length\";\n \"star_generate_indices\" -> \"star_indices_stdout_log\";\n \"sort_annotation_bed\" -> \"annotation_bed\";\n \"bowtie_generate_indices\" -> \"bowtie_indices_stdout_log\";\n \"ribosomal_generate_indices\" -> \"ribosomal_indices_stdout_log\";\n \"prepare_annotation\" -> \"annotation\";\n \"star_generate_indices\" -> \"star_indices_stderr_log\";\n \"annotation_bed_to_bigbed\" -> \"annotation_bed_tbi\";\n \"prepare_annotation\" -> \"annotation_gtf\";\n \"index_fasta\" -> \"fasta_fai_output\";\n \"ribosomal_generate_indices\" -> \"ribosomal_indices_stderr_log\";\n \"extract_cytoband\" -> \"cytoband_output\";\n}\n","licenseLink":"https://spdx.org/licenses/Apache-2.0","permalink":"https://w3id.org/cwl/view/git/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl","packed":false,"visualisationXdot":"/graph/xdot/github.com/datirium/workflows/blob/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl","visualisationPng":"/graph/png/github.com/datirium/workflows/blob/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl","visualisationSvg":"/graph/svg/github.com/datirium/workflows/blob/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl","roBundle":"/robundle/github.com/datirium/workflows/blob/d1bef74924efcb8bfaa00987b3f148d5a192b7a9/workflows/genome-indices.cwl","licenseName":"Apache License 2.0"}