[ { "name": "Megahit-FindMitos-Blast-Annotate-IGV", "docker_name": "megahit-findmitos-blast-annotate-igv", "description": "Find mitochondrial genome ", "version": "0.0.1", "author": "MBB", "options": [ { "name": "results_dir", "type": "output_dir", "value": "\/Results", "label": "Results directory: ", "volumes": [ { "Results": "\/Results" } ] } ], "steps_in": [ { "step_name": "blast_2", "tool_name": "makeblastdb", "rule_name": "makeblastdb", "params": [] }, { "step_name": "assembly", "tool_name": "megahit", "rule_name": "megahit_PE", "params": [ { "input_name": "read", "origin_command": "raw_reads", "origin_name": "read", "origin_step": "input" }, { "input_name": "read2", "origin_command": "raw_reads", "origin_name": "read2", "origin_step": "input" } ] }, { "step_name": "find_mito_scaffold", "tool_name": "mitoz_findmitoscaf", "rule_name": "mitoz_findmitoscaf", "params": [ { "input_name": "fasta", "origin_command": "megahit_PE", "origin_name": "contigs", "origin_step": "assembly" } ] }, { "step_name": "annotation", "tool_name": "mitoz_annotate", "rule_name": "mitoz_annotate_PE", "params": [ { "input_name": "read", "origin_command": "raw_reads", "origin_name": "read", "origin_step": "input" }, { "input_name": "read2", "origin_command": "raw_reads", "origin_name": "read2", "origin_step": "input" }, { "input_name": "fasta", "origin_command": "mitoz_findmitoscaf", "origin_name": "mitogenome", "origin_step": "find_mito_scaffold" } ] }, { "step_name": "blast", "tool_name": "blastn", "rule_name": "blastn", "params": [ { "input_name": "query", "origin_command": "mitoz_findmitoscaf", "origin_name": "mitogenome", "origin_step": "find_mito_scaffold" }, { "input_name": "blastdb", "origin_command": "makeblastdb", "origin_name": "database", "origin_step": "blast_2" } ] }, { "step_name": "visualization", "tool_name": "igv_visualize", "rule_name": "igv_visualize", "params": [ { "input_name": "genome", "origin_command": "mitoz_findmitoscaf", "origin_name": "mitogenome", "origin_step": "find_mito_scaffold" }, { "input_name": "circos_bam", "origin_command": "mitoz_annotate_PE", "origin_name": "circos_bam", "origin_step": "annotation" } ] } ], "steps": [ { "title": "blast_2", "name": "blast_2", "tools": [ "makeblastdb" ], "default": "makeblastdb" }, { "title": "assembly", "name": "assembly", "tools": [ "megahit" ], "default": "megahit" }, { "title": "find_mito_scaffold", "name": "find_mito_scaffold", "tools": [ "mitoz_findmitoscaf" ], "default": "mitoz_findmitoscaf" }, { "title": "annotation", "name": "annotation", "tools": [ "mitoz_annotate" ], "default": "mitoz_annotate" }, { "title": "blast", "name": "blast", "tools": [ "blastn" ], "default": "blastn" }, { "title": "visualization", "name": "visualization", "tools": [ "igv_visualize" ], "default": "igv_visualize" } ], "input": [ "raw_contigs", "raw_reads" ], "params_equals": [ { "remove": "blast__blastn_query" }, { "remove": "blast__blastn_blastdb" } ], "git": "https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/megahit-findmitos-blast-annotate-igv", "json": { "class": "GraphLinksModel", "linkFromPortIdProperty": "fromPort", "linkToPortIdProperty": "toPort", "modelData": { "position": "-482.614990234375 -499" }, "nodeDataArray": [ { "name": "reads", "text": "read", "size2": "", "category": "Data", "strokeWidth": 2, "fill": "#2ecc71", "inservices": [], "outservices": [ { "name": "o1", "type": "reads", "value": "raw_reads", "description": "", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o2", "type": "link", "value": "linkOut" } ], "description": "unknown", "version": "unknown", "key": -3, "loc": "-420 -290" }, { "name": "reads", "text": "read", "size2": "", "category": "Data", "strokeWidth": 2, "fill": "#2ecc71", "inservices": [], "outservices": [ { "name": "o1", "type": "reads", "value": "raw_reads", "description": "", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o2", "type": "link", "value": "linkOut" } ], "description": "unknown", "version": "unknown", "key": -2, "loc": "-420 -60" }, { "name": "megahit_PE", "text": "Megahit PE", "size2": "130 85", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "reads", "value": "read", "description": "", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" }, { "name": "i2", "type": "reads", "value": "read2", "description": "", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "contigs", "value": "contigs", "description": "Result of the assembly", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o2", "type": "link", "value": "linkOut" } ], "description": "An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph", "version": "1.2.1", "key": "4333926610", "loc": "10 -280" }, { "name": "mitoz_findmitoscaf", "text": "Mitoz find mitos scafold", "size2": "230 85", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "contigs", "value": "fasta", "description": "", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "contigs", "value": "mitogenome", "description": "The mitochondrial sequences from each Kmer assembly", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o2", "type": "txt", "value": "readme", "description": "Readme with all output files explained", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o3", "type": "link", "value": "linkOut" } ], "description": "A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes", "version": "2.4-alpha", "key": "1411102249", "loc": "380 -230" }, { "name": "mitoz_annotate_PE", "text": "Mitoz annotate PE", "size2": "195 110", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "reads", "value": "read", "description": "", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" }, { "name": "i2", "type": "reads", "value": "read2", "description": "", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" }, { "name": "i3", "type": "contigs", "value": "fasta", "description": "", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "fa.gbf", "value": "genbank_annots", "description": "The mitochondrial genome in GenBank format", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o2", "type": "txt", "value": "readme", "description": "Readme with all output files explained", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o3", "type": "bams", "value": "circos_bam", "description": "Mapping to determine depth for Circos plot", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o4", "type": "link", "value": "linkOut" } ], "description": "A toolkit for assembly, annotation, and visualization of animal mitochondrial genomes", "version": "2.4-alpha", "key": "3535471919", "loc": "710 -120" }, { "name": "igv_visualize", "text": "Igv visualize", "size2": "155 85", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "contigs", "value": "genome", "description": "", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" }, { "name": "i2", "type": "bams", "value": "circos_bam", "description": "", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "png", "value": "igv_png", "description": "Contig and read coverage visualisation", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o2", "type": "link", "value": "linkOut" } ], "description": "Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations ", "version": "2.6.2", "key": "0142693080", "loc": "1110 -230" }, { "name": "blastn", "text": "blastn", "size2": "125 85", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "contigs", "value": "query", "description": "Fasta query file", "ptype": "IN", "from": "parameter", "list": false, "stroke": "#000000" }, { "name": "i2", "type": "blast_db", "value": "blastdb", "description": "Blast database", "ptype": "IN", "from": "parameter", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "tsv", "value": "blastout", "description": "Blast output", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o2", "type": "link", "value": "linkOut" } ], "description": "BLASTN programs search nucleotide databases using a nucleotide query", "version": "2.12.0", "key": "4337104074", "loc": "900 -420" }, { "name": "makeblastdb", "text": "Make Blast db", "size2": "160 60", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "contigs", "value": "genome_fasta", "description": "Fasta file input", "ptype": "IN", "from": "parameter", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "blast_db", "value": "database", "description": "Blast database", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o2", "type": "link", "value": "linkOut" } ], "description": "Make Blast database", "version": "2.12.0", "key": "0068638460", "loc": "500 -400" }, { "name": "contigs", "text": "contigs", "size2": "", "category": "Data", "strokeWidth": 2, "fill": "#2ecc71", "inservices": [], "outservices": [ { "name": "o1", "type": "contigs", "value": "raw_contigs", "description": "", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o2", "type": "link", "value": "linkOut" } ], "description": "unknown", "version": "unknown", "key": -5, "loc": "-70 -460" } ], "linkDataArray": [ { "from": -3, "to": "4333926610", "fromPort": "raw_reads", "toPort": "read", "points": [ -362.385009765625, -291.5463053385417, -344.385009765625, -291.5463053385417, -211.2647705078125, -291.5463053385417, -211.2647705078125, -288.888916015625, -78.14453125, -288.888916015625, -68.14453125, -288.888916015625 ] }, { "from": -2, "to": "4333926610", "fromPort": "raw_reads", "toPort": "read2", "points": [ -362.385009765625, -61.546305338541664, -352.385009765625, -61.546305338541664, -215.2647705078125, -61.546305338541664, -215.2647705078125, -265.81108398437493, -78.14453125, -265.81108398437493, -68.14453125, -265.81108398437493 ] }, { "from": "4333926610", "to": "1411102249", "fromPort": "contigs", "toPort": "fasta", "points": [ 88.14453125, -277.35, 98.14453125, -277.35, 170, -277.35, 170, -227.35, 241.85546875, -227.35, 251.85546875, -227.35 ] }, { "from": -3, "to": "3535471919", "fromPort": "raw_reads", "toPort": "read", "points": [ -362.385009765625, -285.85369466145835, -352.385009765625, -285.85369466145835, -352.385009765625, -285.85369466145835, -352.385009765625, -141.67783203125, 589.35546875, -141.67783203125, 599.35546875, -141.67783203125 ] }, { "from": -2, "to": "3535471919", "fromPort": "raw_reads", "toPort": "read2", "points": [ -362.385009765625, -55.853694661458334, -344.385009765625, -55.853694661458334, 122.4852294921875, -55.853694661458334, 122.4852294921875, -118.60000000000002, 589.35546875, -118.60000000000002, 599.35546875, -118.60000000000002 ] }, { "from": "1411102249", "to": "3535471919", "fromPort": "mitogenome", "toPort": "fasta", "points": [ 508.14453125, -238.888916015625, 518.14453125, -238.888916015625, 553.75, -238.888916015625, 553.75, -95.52216796875001, 589.35546875, -95.52216796875001, 599.35546875, -95.52216796875001 ] }, { "from": "3535471919", "to": "0142693080", "fromPort": "circos_bam", "toPort": "circos_bam", "points": [ 820.64453125, -95.52216796875001, 830.64453125, -95.52216796875001, 920, -95.52216796875001, 920, -215.811083984375, 1009.35546875, -215.811083984375, 1019.35546875, -215.811083984375 ] }, { "from": "1411102249", "to": "0142693080", "fromPort": "mitogenome", "toPort": "genome", "points": [ 508.14453125, -241.73522135416667, 526.14453125, -241.73522135416667, 767.75, -241.73522135416667, 767.75, -238.888916015625, 1009.35546875, -238.888916015625, 1019.35546875, -238.888916015625 ] }, { "from": "0068638460", "to": "4337104074", "fromPort": "database", "toPort": "blastdb", "points": [ 593.14453125, -396.1, 603.14453125, -396.1, 708.75, -396.1, 708.75, -405.81108398437493, 814.35546875, -405.81108398437493, 824.35546875, -405.81108398437493 ] }, { "from": -5, "to": "0068638460", "fromPort": "raw_contigs", "toPort": "genome_fasta", "points": [ -12.385009765625, -458.70000000000005, -2.385009765625, -458.70000000000005, 197.2352294921875, -458.70000000000005, 197.2352294921875, -396.1, 396.85546875, -396.1, 406.85546875, -396.1 ] }, { "from": "1411102249", "to": "4337104074", "fromPort": "mitogenome", "toPort": "query", "points": [ 508.14453125, -243.1583740234375, 518.14453125, -243.1583740234375, 666.25, -243.1583740234375, 666.25, -428.888916015625, 814.35546875, -428.888916015625, 824.35546875, -428.888916015625 ] } ], "version": 2 }, "yaml": "{\nname: \"Megahit-FindMitos-Blast-Annotate-IGV\",\ndocker_name: \"megahit-findmitos-blast-annotate-igv\",\ndescription: \"Find mitochondrial genome \",\nversion: \"0.0.1\",\nauthor: \"MBB\",\noptions: [\n {\n name: \"results_dir\",\n type: \"output_dir\",\n value: \"\/Results\",\n label: \"Results directory: \",\n volumes: [Results: \"\/Results\"]\n },\n],\nsteps_in: [\n{ step_name: \"blast_2\", tool_name: \"makeblastdb\", rule_name: \"makeblastdb\",\n params: [\n #{ input_name: genome_fasta, origin_command: raw_contigs, origin_name: contigs, origin_step: input}, # This input will be read from the params file (see documentation)\n ]\n},\n{ step_name: \"assembly\", tool_name: \"megahit\", rule_name: \"megahit_PE\",\n params: [\n { input_name: read, origin_command: raw_reads, origin_name: read, origin_step: input},\n { input_name: read2, origin_command: raw_reads, origin_name: read2, origin_step: input},\n ]\n},\n{ step_name: \"find_mito_scaffold\", tool_name: \"mitoz_findmitoscaf\", rule_name: \"mitoz_findmitoscaf\",\n params: [\n { input_name: fasta, origin_command: megahit_PE, origin_name: contigs, origin_step: assembly},\n ]\n},\n{ step_name: \"annotation\", tool_name: \"mitoz_annotate\", rule_name: \"mitoz_annotate_PE\",\n params: [\n { input_name: read, origin_command: raw_reads, origin_name: read, origin_step: input},\n { input_name: read2, origin_command: raw_reads, origin_name: read2, origin_step: input},\n { input_name: fasta, origin_command: mitoz_findmitoscaf, origin_name: mitogenome, origin_step: find_mito_scaffold},\n ]\n},\n{ step_name: \"blast\", tool_name: \"blastn\", rule_name: \"blastn\",\n params: [\n { input_name: query, origin_command: mitoz_findmitoscaf, origin_name: mitogenome, origin_step: find_mito_scaffold},\n { input_name: blastdb, origin_command: makeblastdb, origin_name: database, origin_step: blast_2},\n ]\n},\n{ step_name: \"visualization\", tool_name: \"igv_visualize\", rule_name: \"igv_visualize\",\n params: [\n { input_name: genome, origin_command: mitoz_findmitoscaf, origin_name: mitogenome, origin_step: find_mito_scaffold},\n { input_name: circos_bam, origin_command: mitoz_annotate_PE, origin_name: circos_bam, origin_step: annotation},\n ]\n},\n],\nsteps: [\n { title: \"blast_2\", name: \"blast_2\", tools: [makeblastdb], default: \"makeblastdb\" },\n { title: \"assembly\", name: \"assembly\", tools: [megahit], default: \"megahit\" },\n { title: \"find_mito_scaffold\", name: \"find_mito_scaffold\", tools: [mitoz_findmitoscaf], default: \"mitoz_findmitoscaf\" },\n { title: \"annotation\", name: \"annotation\", tools: [mitoz_annotate], default: \"mitoz_annotate\" },\n { title: \"blast\", name: \"blast\", tools: [blastn], default: \"blastn\" },\n { title: \"visualization\", name: \"visualization\", tools: [igv_visualize], default: \"igv_visualize\" },\n],\ninput: [\"raw_contigs\",\"raw_reads\",],\nparams_equals: [\n { remove: blast__blastn_query},\n { remove: blast__blastn_blastdb},\n\n]\n}\n" } ]