[ { "name": "Orientator_Khalid", "docker_name": "Orientator_Khalid", "description": "Thanks to outgroups, this pipeline determine and write the Ancestral Allele of biallelic variant in a VCF", "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", "tool_name": "makeblastdb", "rule_name": "makeblastdb", "params": [] }, { "step_name": "blast_2", "tool_name": "makeblastdb", "rule_name": "makeblastdb", "params": [] }, { "step_name": "blast_3", "tool_name": "makeblastdb", "rule_name": "makeblastdb", "params": [] }, { "step_name": "vcf_postprocess_3", "tool_name": "vcftools_allelic_variants_count_sfs", "rule_name": "vcftools_allelic_variants_count_sfs", "params": [ { "input_name": "vcf", "origin_command": "raw_vcf_file", "origin_name": "vcf_file", "origin_step": "input" } ] }, { "step_name": "vcf_postprocess", "tool_name": "BEDTools_vcf_flanking_sequence", "rule_name": "BEDTools_vcf_flanking_sequence", "params": [ { "input_name": "vcf", "origin_command": "raw_vcf_file", "origin_name": "vcf_file", "origin_step": "input" }, { "input_name": "genome_fasta", "origin_command": "raw_fasta_file", "origin_name": "fasta_file", "origin_step": "input" } ] }, { "step_name": "blast_4", "tool_name": "blast_snp2outgroup", "rule_name": "blast_snp2outgroup", "params": [ { "input_name": "query", "origin_command": "BEDTools_vcf_flanking_sequence", "origin_name": "fasta", "origin_step": "vcf_postprocess" }, { "input_name": "blastdb_dir", "origin_command": "makeblastdb", "origin_name": "database", "origin_step": "blast" } ] }, { "step_name": "blast_5", "tool_name": "blast_snp2outgroup", "rule_name": "blast_snp2outgroup", "params": [ { "input_name": "query", "origin_command": "BEDTools_vcf_flanking_sequence", "origin_name": "fasta", "origin_step": "vcf_postprocess" }, { "input_name": "blastdb_dir", "origin_command": "makeblastdb", "origin_name": "database", "origin_step": "blast_2" } ] }, { "step_name": "blast_6", "tool_name": "blast_snp2outgroup", "rule_name": "blast_snp2outgroup", "params": [ { "input_name": "query", "origin_command": "BEDTools_vcf_flanking_sequence", "origin_name": "fasta", "origin_step": "vcf_postprocess" }, { "input_name": "blastdb_dir", "origin_command": "makeblastdb", "origin_name": "database", "origin_step": "blast_3" } ] }, { "step_name": "other_2", "tool_name": "snom", "rule_name": "snom", "params": [ { "input_name": "blast_out_snom", "origin_command": "blast_snp2outgroup", "origin_name": "blastout", "origin_step": "blast_4" } ] }, { "step_name": "other_3", "tool_name": "snom", "rule_name": "snom", "params": [ { "input_name": "blast_out_snom", "origin_command": "blast_snp2outgroup", "origin_name": "blastout", "origin_step": "blast_5" } ] }, { "step_name": "other_4", "tool_name": "snom", "rule_name": "snom", "params": [ { "input_name": "blast_out_snom", "origin_command": "blast_snp2outgroup", "origin_name": "blastout", "origin_step": "blast_6" } ] }, { "step_name": "other", "tool_name": "est_sfs", "rule_name": "est_sfs", "params": [ { "input_name": "sfs_vcf", "origin_command": "vcftools_allelic_variants_count_sfs", "origin_name": "sfs", "origin_step": "vcf_postprocess_3" }, { "input_name": "sfs_outgroup1", "origin_command": "snom", "origin_name": "sfs_outgroup", "origin_step": "other_2" }, { "input_name": "sfs_outgroup2", "origin_command": "snom", "origin_name": "sfs_outgroup", "origin_step": "other_3" }, { "input_name": "sfs_outgroup3", "origin_command": "snom", "origin_name": "sfs_outgroup", "origin_step": "other_4" } ] }, { "step_name": "vcf_postprocess_2", "tool_name": "vcf_annotate", "rule_name": "vcf_annotate", "params": [ { "input_name": "vcf", "origin_command": "raw_vcf_file", "origin_name": "vcf_file", "origin_step": "input" }, { "input_name": "tsv", "origin_command": "est_sfs", "origin_name": "aatsv", "origin_step": "other" } ] } ], "steps": [ { "title": "blast", "name": "blast", "tools": [ "makeblastdb" ], "default": "makeblastdb" }, { "title": "blast_2", "name": "blast_2", "tools": [ "makeblastdb" ], "default": "makeblastdb" }, { "title": "blast_3", "name": "blast_3", "tools": [ "makeblastdb" ], "default": "makeblastdb" }, { "title": "vcf_postprocess_3", "name": "vcf_postprocess_3", "tools": [ "vcftools_allelic_variants_count_sfs" ], "default": "vcftools_allelic_variants_count_sfs" }, { "title": "vcf_postprocess", "name": "vcf_postprocess", "tools": [ "BEDTools_vcf_flanking_sequence" ], "default": "BEDTools_vcf_flanking_sequence" }, { "title": "blast_4", "name": "blast_4", "tools": [ "blast_snp2outgroup" ], "default": "blast_snp2outgroup" }, { "title": "blast_5", "name": "blast_5", "tools": [ "blast_snp2outgroup" ], "default": "blast_snp2outgroup" }, { "title": "blast_6", "name": "blast_6", "tools": [ "blast_snp2outgroup" ], "default": "blast_snp2outgroup" }, { "title": "other_2", "name": "other_2", "tools": [ "snom" ], "default": "snom" }, { "title": "other_3", "name": "other_3", "tools": [ "snom" ], "default": "snom" }, { "title": "other_4", "name": "other_4", "tools": [ "snom" ], "default": "snom" }, { "title": "other", "name": "other", "tools": [ "est_sfs" ], "default": "est_sfs" }, { "title": "vcf_postprocess_2", "name": "vcf_postprocess_2", "tools": [ "vcf_annotate" ], "default": "vcf_annotate" } ], "input": [ "raw_vcf_file", "raw_fasta_file" ], "params_equals": [ { "param_A": "vcf_postprocess__BEDTools_vcf_flanking_sequence_vcf", "param_B": "vcf_postprocess_3__vcftools_allelic_variants_count_sfs_vcf" }, { "param_A": "vcf_postprocess__BEDTools_vcf_flanking_sequence_vcf", "param_B": "vcf_postprocess_2__vcf_annotate_vcf" }, { "remove": "blast_4__blast_snp2outgroup_query" }, { "remove": "blast_4__blast_snp2outgroup_blastdb_dir" }, { "remove": "blast_5__blast_snp2outgroup_query" }, { "remove": "blast_5__blast_snp2outgroup_blastdb_dir" }, { "remove": "blast_6__blast_snp2outgroup_query" }, { "remove": "blast_6__blast_snp2outgroup_blastdb_dir" }, { "remove": "other_2__snom_blast_out_snom" }, { "remove": "other_3__snom_blast_out_snom" }, { "remove": "other_4__snom_blast_out_snom" } ], "git": "https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/Orientator_Khalid", "json": { "class": "GraphLinksModel", "linkFromPortIdProperty": "fromPort", "linkToPortIdProperty": "toPort", "nodeDataArray": [ { "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": "2.14.0", "key": "4336616510", "loc": "20 -60" }, { "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": "2.14.0", "key": "43366165102", "loc": "20 70" }, { "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": "2.14.0", "key": "43366165103", "loc": "20 190" }, { "name": "BEDTools_vcf_flanking_sequence", "text": "BEDTools vcf flanking sequence", "size2": "295 85", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "vcf_file", "value": "vcf", "description": "Variant Calling Format (vcf) file", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" }, { "name": "i2", "type": "fasta_file", "value": "genome_fasta", "description": "Fasta reference", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "bed", "value": "bed", "description": "Bed", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o2", "type": "fasta_file", "value": "fasta", "description": "flanking sequence fasta file of the variant (in vcf)", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o3", "type": "link", "value": "linkOut" } ], "description": "BEDTools to obtain the flanking sequence of each variant in the VCF.", "version": "2.31", "key": "3720802199", "loc": "60 -280" }, { "name": "vcf_annotate", "text": "vcf_annotate", "size2": "150 85", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "vcf_file", "value": "vcf", "description": "Variant Calling Format (vcf) file", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" }, { "name": "i2", "type": "tsv", "value": "tsv", "description": "TSV file with CHR POS0 INFO_ANNOTATION", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "vcf", "value": "vcf_annot", "description": "vcf file whith annotation append", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o2", "type": "link", "value": "linkOut" } ], "description": "BCFtools annotate to append a new INFO in a vcf.", "version": "1.17", "key": "8987444290", "loc": "910 -360" }, { "name": "vcftools_allelic_variants_count_sfs", "text": "vcftools allelic variants count sfs", "size2": "310 85", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "vcf_file", "value": "vcf", "description": "Variant Calling Format (vcf) file", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "tsv", "value": "frq", "description": "tsv file with allele frequency count", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o2", "type": "sfs", "value": "sfs", "description": "vcf with allele frequency count as est-sfs format", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o3", "type": "link", "value": "linkOut" } ], "description": "VCFtools to count the allele frequency of each variant and convert to partial est-sfs format input.", "version": "0.1.16", "key": "6237943211", "loc": "70 -440" }, { "name": "est_sfs", "text": "est_sfs", "size2": "125 135", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "sfs", "value": "sfs_vcf", "description": "(Required) sfs count file generate from vcf", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" }, { "name": "i2", "type": "sfs", "value": "sfs_outgroup1", "description": "(Required) sfs count file from outgroup1", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" }, { "name": "i3", "type": "sfs", "value": "sfs_outgroup2", "description": "(Optional) sfs count file from outgroup2", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" }, { "name": "i4", "type": "sfs", "value": "sfs_outgroup3", "description": "(Optional) sfs count file from outgroup3", "ptype": "IN", "from": "", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "tsv", "value": "aatsv", "description": "TSV file with CHR POS0 AA (Ancestral Allele) informations", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" }, { "name": "o2", "type": "tsv", "value": "est_sfs_output_aa", "description": "est sfs output with est-sfs input information, pvalue information and ancestral allele information.", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o3", "type": "link", "value": "linkOut" } ], "description": "BLAST programs search nucleotide databases using a nucleotide query", "version": "2.04", "key": "0029200891", "loc": "720 -260" }, { "name": "fasta_file", "text": "fasta_file", "size2": "", "category": "Data", "strokeWidth": 2, "fill": "#2ecc71", "inservices": [], "outservices": [ { "name": "o1", "type": "fasta_file", "value": "raw_fasta_file", "description": "", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o2", "type": "link", "value": "linkOut" } ], "description": "unknown", "version": "unknown", "key": -6, "loc": "-280 -270" }, { "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": -7, "loc": "-280 -60" }, { "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": -13, "loc": "-280 70" }, { "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": -14, "loc": "-280 200" }, { "name": "vcf_file", "text": "vcf_file", "size2": "", "category": "Data", "strokeWidth": 2, "fill": "#2ecc71", "inservices": [], "outservices": [ { "name": "o1", "type": "vcf_file", "value": "raw_vcf_file", "description": "", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o2", "type": "link", "value": "linkOut" } ], "description": "unknown", "version": "unknown", "key": -10, "loc": "-280 -370" }, { "name": "blast_snp2outgroup", "text": "blast_snp2outgroup", "size2": "175 85", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "fasta_file", "value": "query", "description": "Fasta query file", "ptype": "IN", "from": "parameter", "list": false, "stroke": "#000000" }, { "name": "i2", "type": "blast_db", "value": "blastdb_dir", "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": "BLAST programs search nucleotide databases using a nucleotide query", "version": "2.14.0", "key": "5690700601", "loc": "340 -70" }, { "name": "blast_snp2outgroup", "text": "blast_snp2outgroup", "size2": "175 85", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "fasta_file", "value": "query", "description": "Fasta query file", "ptype": "IN", "from": "parameter", "list": false, "stroke": "#000000" }, { "name": "i2", "type": "blast_db", "value": "blastdb_dir", "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": "BLAST programs search nucleotide databases using a nucleotide query", "version": "2.14.0", "key": "56907006012", "loc": "340 60" }, { "name": "blast_snp2outgroup", "text": "blast_snp2outgroup", "size2": "175 85", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "fasta_file", "value": "query", "description": "Fasta query file", "ptype": "IN", "from": "parameter", "list": false, "stroke": "#000000" }, { "name": "i2", "type": "blast_db", "value": "blastdb_dir", "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": "BLAST programs search nucleotide databases using a nucleotide query", "version": "2.14.0", "key": "56907006013", "loc": "340 180" }, { "name": "snom", "text": "snom", "size2": "125 60", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "tsv", "value": "blast_out_snom", "description": "TSV with seqid, qstart qend btop, qseq, sseq informations", "ptype": "IN", "from": "parameter", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "sfs", "value": "sfs_outgroup", "description": "specific nucleotide count as est-sfs outgroup format", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o2", "type": "link", "value": "linkOut" } ], "description": "Find out homologous of specific base of a query sequence in blast results", "version": "0.1.0", "key": "4476603955", "loc": "540 -70" }, { "name": "snom", "text": "snom", "size2": "125 60", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "tsv", "value": "blast_out_snom", "description": "TSV with seqid, qstart qend btop, qseq, sseq informations", "ptype": "IN", "from": "parameter", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "sfs", "value": "sfs_outgroup", "description": "specific nucleotide count as est-sfs outgroup format", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o2", "type": "link", "value": "linkOut" } ], "description": "Find out homologous of specific base of a query sequence in blast results", "version": "0.1.0", "key": "44766039552", "loc": "550 60" }, { "name": "snom", "text": "snom", "size2": "125 60", "category": "Tool", "strokeWidth": 2, "fill": "#3498db", "inservices": [ { "name": "i1", "type": "tsv", "value": "blast_out_snom", "description": "TSV with seqid, qstart qend btop, qseq, sseq informations", "ptype": "IN", "from": "parameter", "list": false, "stroke": "#000000" } ], "outservices": [ { "name": "o1", "type": "sfs", "value": "sfs_outgroup", "description": "specific nucleotide count as est-sfs outgroup format", "ptype": "OUT", "from": "", "list": false, "stroke": "#000000" } ], "outservices2": [ { "name": "o2", "type": "link", "value": "linkOut" } ], "description": "Find out homologous of specific base of a query sequence in blast results", "version": "0.1.0", "key": "44766039553", "loc": "550 180" } ], "linkDataArray": [ { "from": "0029200891", "to": "8987444290", "fromPort": "aatsv", "toPort": "tsv", "points": [ 796.5250000953674, -271.6408330440521, 806.5250000953674, -271.6408330440521, 808.75, -271.6408330440521, 808.75, -345.55916695594783, 810.9749999046326, -345.55916695594783, 820.9749999046326, -345.55916695594783 ] }, { "from": "6237943211", "to": "0029200891", "fromPort": "sfs", "toPort": "sfs_vcf", "points": [ 239.02500009536743, -425.55916695594783, 249.02500009536743, -425.55916695594783, 441.25, -425.55916695594783, 441.25, -295.2224991321564, 633.4749999046326, -295.2224991321564, 643.4749999046326, -295.2224991321564 ] }, { "from": -6, "to": "3720802199", "fromPort": "raw_fasta_file", "toPort": "genome_fasta", "points": [ -221.94583320617676, -268.7, -211.94583320617676, -268.7, -161.7354166507721, -268.7, -161.7354166507721, -265.55916695594783, -111.52500009536743, -265.55916695594783, -101.52500009536743, -265.55916695594783 ] }, { "from": -7, "to": "4336616510", "fromPort": "raw_contigs", "toPort": "genome_fasta", "points": [ -221.94583320617676, -58.7, -211.94583320617676, -58.7, -147.9854166507721, -58.7, -147.9854166507721, -56.099999999999994, -84.02500009536743, -56.099999999999994, -74.02500009536743, -56.099999999999994 ] }, { "from": -14, "to": "43366165103", "fromPort": "raw_contigs", "toPort": "genome_fasta", "points": [ -221.94583320617676, 201.3, -211.94583320617676, 201.3, -147.9854166507721, 201.3, -147.9854166507721, 193.89999999999998, -84.02500009536743, 193.89999999999998, -74.02500009536743, 193.89999999999998 ] }, { "from": -13, "to": "43366165102", "fromPort": "raw_contigs", "toPort": "genome_fasta", "points": [ -221.94583320617676, 71.3, -211.94583320617676, 71.3, -147.9854166507721, 71.3, -147.9854166507721, 73.9, -84.02500009536743, 73.9, -74.02500009536743, 73.9 ] }, { "from": -10, "to": "3720802199", "fromPort": "raw_vcf_file", "toPort": "vcf", "points": [ -221.94583320617676, -364.3045834779739, -211.94583320617676, -364.3045834779739, -161.7354166507721, -364.3045834779739, -161.7354166507721, -289.1408330440521, -111.52500009536743, -289.1408330440521, -101.52500009536743, -289.1408330440521 ] }, { "from": -10, "to": "6237943211", "fromPort": "raw_vcf_file", "toPort": "vcf", "points": [ -221.94583320617676, -373.0954165220261, -211.94583320617676, -373.0954165220261, -160.4854166507721, -373.0954165220261, -160.4854166507721, -437.34999999999997, -109.02500009536743, -437.34999999999997, -99.02500009536743, -437.34999999999997 ] }, { "from": -10, "to": "8987444290", "fromPort": "raw_vcf_file", "toPort": "vcf", "points": [ -221.94583320617676, -368.7, -203.94583320617676, -368.7, 303.5145833492279, -368.7, 303.5145833492279, -369.1408330440521, 810.9749999046326, -369.1408330440521, 820.9749999046326, -369.1408330440521 ] }, { "from": "4336616510", "to": "5690700601", "fromPort": "database", "toPort": "blastdb_dir", "points": [ 114.02500009536743, -56.099999999999994, 124.02500009536743, -56.099999999999994, 176.25, -56.099999999999994, 176.25, -55.55916695594787, 228.47499990463257, -55.55916695594787, 238.47499990463257, -55.55916695594787 ] }, { "from": "43366165102", "to": "56907006012", "fromPort": "database", "toPort": "blastdb_dir", "points": [ 114.02500009536743, 73.9, 124.02500009536743, 73.9, 176.25, 73.9, 176.25, 74.44083304405213, 228.47499990463257, 74.44083304405213, 238.47499990463257, 74.44083304405213 ] }, { "from": "43366165103", "to": "56907006013", "fromPort": "database", "toPort": "blastdb_dir", "points": [ 114.02500009536743, 193.89999999999998, 124.02500009536743, 193.89999999999998, 176.25, 193.89999999999998, 176.25, 194.4408330440521, 228.47499990463257, 194.4408330440521, 238.47499990463257, 194.4408330440521 ] }, { "from": "3720802199", "to": "5690700601", "fromPort": "fasta", "toPort": "query", "points": [ 221.52500009536743, -265.55916695594783, 231.52500009536743, -265.55916695594783, 231.52500009536743, -175, 228.47499990463257, -175, 228.47499990463257, -79.14083304405213, 238.47499990463257, -79.14083304405213 ] }, { "from": "3720802199", "to": "56907006012", "fromPort": "fasta", "toPort": "query", "points": [ 221.52500009536743, -262.6288892745971, 231.52500009536743, -262.6288892745971, 231.52500009536743, -110, 228.47499990463257, -110, 228.47499990463257, 50.85916695594787, 238.47499990463257, 50.85916695594787 ] }, { "from": "3720802199", "to": "56907006013", "fromPort": "fasta", "toPort": "query", "points": [ 221.52500009536743, -261.1637504339218, 231.52500009536743, -261.1637504339218, 231.52500009536743, -50, 228.47499990463257, -50, 228.47499990463257, 170.8591669559479, 238.47499990463257, 170.8591669559479 ] }, { "from": "4476603955", "to": "0029200891", "fromPort": "sfs_outgroup", "toPort": "sfs_outgroup1", "points": [ 616.5250000953674, -66.1, 626.5250000953674, -66.1, 630, -66.1, 630, -271.6408330440521, 633.4749999046326, -271.6408330440521, 643.4749999046326, -271.6408330440521 ] }, { "from": "5690700601", "to": "4476603955", "fromPort": "blastout", "toPort": "blast_out_snom", "points": [ 441.52500009536743, -67.35000000000001, 451.52500009536743, -67.35000000000001, 452.5, -67.35000000000001, 452.5, -66.1, 453.47499990463257, -66.1, 463.47499990463257, -66.1 ] }, { "from": "56907006012", "to": "44766039552", "fromPort": "blastout", "toPort": "blast_out_snom", "points": [ 441.52500009536743, 62.64999999999999, 451.52500009536743, 62.64999999999999, 457.5, 62.64999999999999, 457.5, 63.90000000000001, 463.47499990463257, 63.90000000000001, 473.47499990463257, 63.90000000000001 ] }, { "from": "56907006013", "to": "44766039553", "fromPort": "blastout", "toPort": "blast_out_snom", "points": [ 441.52500009536743, 182.64999999999998, 451.52500009536743, 182.64999999999998, 457.5, 182.64999999999998, 457.5, 183.89999999999998, 463.47499990463257, 183.89999999999998, 473.47499990463257, 183.89999999999998 ] }, { "from": "44766039552", "to": "0029200891", "fromPort": "sfs_outgroup", "toPort": "sfs_outgroup2", "points": [ 626.5250000953674, 63.90000000000001, 636.5250000953674, 63.90000000000001, 636.5250000953674, -81.25, 633.4749999046326, -81.25, 633.4749999046326, -248.0591669559479, 643.4749999046326, -248.0591669559479 ] }, { "from": "44766039553", "to": "0029200891", "fromPort": "sfs_outgroup", "toPort": "sfs_outgroup3", "points": [ 626.5250000953674, 183.89999999999998, 636.5250000953674, 183.89999999999998, 636.5250000953674, -21.25, 633.4749999046326, -21.25, 633.4749999046326, -224.47750086784362, 643.4749999046326, -224.47750086784362 ] } ], "version": 2 }, "yaml": "{\r\nname: \"Orientator_Khalid\",\r\ndocker_name: \"Orientator_Khalid\",\r\ndescription: \"Thanks to outgroups, this pipeline determine and write the Ancestral Allele of biallelic variant in a VCF\",\r\nversion: \"0.0.1\",\r\nauthor: \"MBB\",\r\noptions: [\r\n {\r\n name: \"results_dir\",\r\n type: \"output_dir\",\r\n value: \"\/Results\",\r\n label: \"Results directory: \",\r\n volumes: [Results: \"\/Results\"]\r\n },\r\n],\r\nsteps_in: [\r\n{ step_name: \"blast\", tool_name: \"makeblastdb\", rule_name: \"makeblastdb\",\r\n params: [\r\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)\r\n ]\r\n},\r\n{ step_name: \"blast_2\", tool_name: \"makeblastdb\", rule_name: \"makeblastdb\",\r\n params: [\r\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)\r\n ]\r\n},\r\n{ step_name: \"blast_3\", tool_name: \"makeblastdb\", rule_name: \"makeblastdb\",\r\n params: [\r\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)\r\n ]\r\n},\r\n{ step_name: \"vcf_postprocess_3\", tool_name: \"vcftools_allelic_variants_count_sfs\", rule_name: \"vcftools_allelic_variants_count_sfs\",\r\n params: [\r\n { input_name: vcf, origin_command: raw_vcf_file, origin_name: vcf_file, origin_step: input},\r\n ]\r\n},\r\n{ step_name: \"vcf_postprocess\", tool_name: \"BEDTools_vcf_flanking_sequence\", rule_name: \"BEDTools_vcf_flanking_sequence\",\r\n params: [\r\n { input_name: vcf, origin_command: raw_vcf_file, origin_name: vcf_file, origin_step: input},\r\n { input_name: genome_fasta, origin_command: raw_fasta_file, origin_name: fasta_file, origin_step: input},\r\n ]\r\n},\r\n{ step_name: \"blast_4\", tool_name: \"blast_snp2outgroup\", rule_name: \"blast_snp2outgroup\",\r\n params: [\r\n { input_name: query, origin_command: BEDTools_vcf_flanking_sequence, origin_name: fasta, origin_step: vcf_postprocess},\r\n { input_name: blastdb_dir, origin_command: makeblastdb, origin_name: database, origin_step: blast},\r\n ]\r\n},\r\n{ step_name: \"blast_5\", tool_name: \"blast_snp2outgroup\", rule_name: \"blast_snp2outgroup\",\r\n params: [\r\n { input_name: query, origin_command: BEDTools_vcf_flanking_sequence, origin_name: fasta, origin_step: vcf_postprocess},\r\n { input_name: blastdb_dir, origin_command: makeblastdb, origin_name: database, origin_step: blast_2},\r\n ]\r\n},\r\n{ step_name: \"blast_6\", tool_name: \"blast_snp2outgroup\", rule_name: \"blast_snp2outgroup\",\r\n params: [\r\n { input_name: query, origin_command: BEDTools_vcf_flanking_sequence, origin_name: fasta, origin_step: vcf_postprocess},\r\n { input_name: blastdb_dir, origin_command: makeblastdb, origin_name: database, origin_step: blast_3},\r\n ]\r\n},\r\n{ step_name: \"other_2\", tool_name: \"snom\", rule_name: \"snom\",\r\n params: [\r\n { input_name: blast_out_snom, origin_command: blast_snp2outgroup, origin_name: blastout, origin_step: blast_4},\r\n ]\r\n},\r\n{ step_name: \"other_3\", tool_name: \"snom\", rule_name: \"snom\",\r\n params: [\r\n { input_name: blast_out_snom, origin_command: blast_snp2outgroup, origin_name: blastout, origin_step: blast_5},\r\n ]\r\n},\r\n{ step_name: \"other_4\", tool_name: \"snom\", rule_name: \"snom\",\r\n params: [\r\n { input_name: blast_out_snom, origin_command: blast_snp2outgroup, origin_name: blastout, origin_step: blast_6},\r\n ]\r\n},\r\n{ step_name: \"other\", tool_name: \"est_sfs\", rule_name: \"est_sfs\",\r\n params: [\r\n { input_name: sfs_vcf, origin_command: vcftools_allelic_variants_count_sfs, origin_name: sfs, origin_step: vcf_postprocess_3},\r\n { input_name: sfs_outgroup1, origin_command: snom, origin_name: sfs_outgroup, origin_step: other_2},\r\n { input_name: sfs_outgroup2, origin_command: snom, origin_name: sfs_outgroup, origin_step: other_3},\r\n { input_name: sfs_outgroup3, origin_command: snom, origin_name: sfs_outgroup, origin_step: other_4},\r\n ]\r\n},\r\n{ step_name: \"vcf_postprocess_2\", tool_name: \"vcf_annotate\", rule_name: \"vcf_annotate\",\r\n params: [\r\n { input_name: vcf, origin_command: raw_vcf_file, origin_name: vcf_file, origin_step: input},\r\n { input_name: tsv, origin_command: est_sfs, origin_name: aatsv, origin_step: other},\r\n ]\r\n},\r\n],\r\nsteps: [\r\n { title: \"blast\", name: \"blast\", tools: [makeblastdb], default: \"makeblastdb\" },\r\n { title: \"blast_2\", name: \"blast_2\", tools: [makeblastdb], default: \"makeblastdb\" },\r\n { title: \"blast_3\", name: \"blast_3\", tools: [makeblastdb], default: \"makeblastdb\" },\r\n { title: \"vcf_postprocess_3\", name: \"vcf_postprocess_3\", tools: [vcftools_allelic_variants_count_sfs], default: \"vcftools_allelic_variants_count_sfs\" },\r\n { title: \"vcf_postprocess\", name: \"vcf_postprocess\", tools: [BEDTools_vcf_flanking_sequence], default: \"BEDTools_vcf_flanking_sequence\" },\r\n { title: \"blast_4\", name: \"blast_4\", tools: [blast_snp2outgroup], default: \"blast_snp2outgroup\" },\r\n { title: \"blast_5\", name: \"blast_5\", tools: [blast_snp2outgroup], default: \"blast_snp2outgroup\" },\r\n { title: \"blast_6\", name: \"blast_6\", tools: [blast_snp2outgroup], default: \"blast_snp2outgroup\" },\r\n { title: \"other_2\", name: \"other_2\", tools: [snom], default: \"snom\" },\r\n { title: \"other_3\", name: \"other_3\", tools: [snom], default: \"snom\" },\r\n { title: \"other_4\", name: \"other_4\", tools: [snom], default: \"snom\" },\r\n { title: \"other\", name: \"other\", tools: [est_sfs], default: \"est_sfs\" },\r\n { title: \"vcf_postprocess_2\", name: \"vcf_postprocess_2\", tools: [vcf_annotate], default: \"vcf_annotate\" },\r\n],\r\ninput: [\"raw_vcf_file\",\"raw_fasta_file\",],\r\nparams_equals: [\r\n { param_A: \"vcf_postprocess__BEDTools_vcf_flanking_sequence_vcf\", param_B: \"vcf_postprocess_3__vcftools_allelic_variants_count_sfs_vcf\"},\r\n { param_A: \"vcf_postprocess__BEDTools_vcf_flanking_sequence_vcf\", param_B: \"vcf_postprocess_2__vcf_annotate_vcf\"},\r\n { remove: blast_4__blast_snp2outgroup_query},\r\n { remove: blast_4__blast_snp2outgroup_blastdb_dir},\r\n { remove: blast_5__blast_snp2outgroup_query},\r\n { remove: blast_5__blast_snp2outgroup_blastdb_dir},\r\n { remove: blast_6__blast_snp2outgroup_query},\r\n { remove: blast_6__blast_snp2outgroup_blastdb_dir},\r\n { remove: other_2__snom_blast_out_snom},\r\n { remove: other_3__snom_blast_out_snom},\r\n { remove: other_4__snom_blast_out_snom},\r\n\r\n]\r\n}\r\n" } ]