[
    {
        "name": "Capture_UCE",
        "docker_name": "capture_uce",
        "description": "",
        "version": "0.0.1",
        "author": "MBB",
        "input": "raw_reads",
        "steps": [
            {
                "title": "Quality control",
                "name": "quality_control",
                "tools": [
                    "fastqc"
                ],
                "default": "fastqc"
            },
            {
                "title": "Quality filtering and adapter trimming",
                "name": "qcfilter_adaptertrim",
                "tools": [
                    "trimmomatic"
                ],
                "default": "trimmomatic"
            },
            {
                "title": "Merge of overlapping reads",
                "name": "merge_overlapps",
                "tools": [
                    "flash"
                ],
                "default": "flash"
            },
            {
                "title": "Demultiplexing",
                "name": "demultiplexing",
                "tools": [
                    "demultiplexing_astrid_cruaud"
                ],
                "default": "demultiplexing_astrid_cruaud"
            },
            {
                "title": "Assembling",
                "name": "assembling",
                "tools": [
                    "velvet"
                ],
                "default": "velvet"
            },
            {
                "title": "Contigs map to UCEs references",
                "name": "contigmaptouce",
                "tools": [
                    "lastz"
                ],
                "default": "lastz"
            },
            {
                "title": "Mapping check before filter",
                "name": "mapping_check_bf",
                "tools": [
                    "samtools_stats"
                ],
                "default": "samtools_stats"
            },
            {
                "title": "Mapping check after filter",
                "name": "mapping_check_af",
                "tools": [
                    "samtools_stats"
                ],
                "default": "samtools_stats"
            },
            {
                "title": "Convert to phylip",
                "name": "convert_to_phylip",
                "tools": [
                    "sam_to_phylip"
                ],
                "default": "sam_to_phylip"
            }
        ],
        "options": [
            {
                "name": "results_dir",
                "type": "output_dir",
                "value": "\/Results",
                "label": "Results directory: ",
                "volumes": [
                    {
                        "Results": "\/Results"
                    }
                ]
            }
        ],
        "steps_in": [
            {
                "step_name": "quality_control",
                "tool_name": "fastqc",
                "rule_name": "fastqc_PE",
                "params": [
                    {
                        "input_name": "read",
                        "origin_step": "",
                        "origin_command": "raw_reads",
                        "origin_name": "read"
                    },
                    {
                        "input_name": "read2",
                        "origin_step": "",
                        "origin_command": "raw_reads",
                        "origin_name": "read2"
                    }
                ]
            },
            {
                "step_name": "qcfilter_adaptertrim",
                "tool_name": "trimmomatic",
                "rule_name": "trimmomatic_PE",
                "params": [
                    {
                        "input_name": "read",
                        "origin_step": "",
                        "origin_command": "raw_reads",
                        "origin_name": "read"
                    },
                    {
                        "input_name": "read2",
                        "origin_step": "",
                        "origin_command": "raw_reads",
                        "origin_name": "read2"
                    }
                ]
            },
            {
                "step_name": "merge_overlapps",
                "tool_name": "flash",
                "rule_name": "flash",
                "params": [
                    {
                        "input_name": "read",
                        "origin_step": "qcfilter_adaptertrim",
                        "origin_command": "trimmomatic_PE",
                        "origin_name": "readFP"
                    },
                    {
                        "input_name": "read2",
                        "origin_step": "qcfilter_adaptertrim",
                        "origin_command": "trimmomatic_PE",
                        "origin_name": "readRP"
                    }
                ]
            },
            {
                "step_name": "demultiplexing",
                "tool_name": "demultiplexing_astrid_cruaud",
                "rule_name": "demultiplexing_astrid_cruaud",
                "params": [
                    {
                        "input_name": "extended_frags",
                        "origin_step": "merge_overlapps",
                        "origin_command": "flash",
                        "origin_name": "extendedFrags"
                    }
                ]
            },
            {
                "step_name": "assembling",
                "tool_name": "velvet",
                "rule_name": "velvet",
                "params": [
                    {
                        "input_name": "merged_reads",
                        "origin_step": "demultiplexing",
                        "origin_command": "demultiplexing_astrid_cruaud",
                        "origin_name": "demultiplexed"
                    }
                ]
            },
            {
                "step_name": "contigmaptouce",
                "tool_name": "lastz",
                "rule_name": "lastz",
                "params": [
                    {
                        "input_name": "contigs",
                        "origin_step": "assembling",
                        "origin_command": "velvet",
                        "origin_name": "contigs"
                    }
                ]
            },
            {
                "step_name": "mapping_check_bf",
                "tool_name": "samtools_stats",
                "rule_name": "samtools_stats",
                "params": [
                    {
                        "input_name": "bam",
                        "origin_step": "contigmaptouce",
                        "origin_command": "lastz",
                        "origin_name": "align_on_ref"
                    }
                ]
            },
            {
                "step_name": "mapping_check_af",
                "tool_name": "samtools_stats",
                "rule_name": "samtools_stats",
                "params": [
                    {
                        "input_name": "bam",
                        "origin_step": "contigmaptouce",
                        "origin_command": "lastz",
                        "origin_name": "filtered"
                    }
                ]
            },
            {
                "step_name": "convert_to_phylip",
                "tool_name": "sam_to_phylip",
                "rule_name": "sam_to_phylip",
                "params": [
                    {
                        "input_name": "sams",
                        "origin_step": "contigmaptouce",
                        "origin_command": "lastz",
                        "origin_name": "filtered"
                    }
                ]
            }
        ],
        "git": "https:\/\/gitlab.mbb.univ-montp2.fr\/khalid\/capture_uce",
        "json": {
            "class": "GraphLinksModel",
            "linkFromPortIdProperty": "fromPort",
            "linkToPortIdProperty": "toPort",
            "modelData": {
                "position": "-623.0541667938232 -342"
            },
            "nodeDataArray": [
                {
                    "name": "read",
                    "text": "reads",
                    "category": "Data",
                    "figure": "FramedRectangle",
                    "fill": "#2ecc71",
                    "strokeWidth": 2,
                    "outservices": [
                        {
                            "name": "o1",
                            "type": "reads",
                            "value": "raw_reads"
                        }
                    ],
                    "key": -3,
                    "loc": "-550 -210"
                },
                {
                    "name": "read",
                    "text": "reads",
                    "category": "Data",
                    "figure": "FramedRectangle",
                    "fill": "#2ecc71",
                    "strokeWidth": 2,
                    "outservices": [
                        {
                            "name": "o1",
                            "type": "reads",
                            "value": "raw_reads"
                        }
                    ],
                    "key": -2,
                    "loc": "-560 260"
                },
                {
                    "name": "fastp_PE",
                    "text": "Fastp PE",
                    "size2": "130 135",
                    "category": "Tool",
                    "strokeWidth": 2,
                    "fill": "#3498db",
                    "inservices": [
                        {
                            "name": "i1",
                            "type": "reads",
                            "value": "read",
                            "description": "",
                            "ptype": "IN"
                        },
                        {
                            "name": "i2",
                            "type": "reads",
                            "value": "read2",
                            "description": "",
                            "ptype": "IN"
                        }
                    ],
                    "outservices": [
                        {
                            "name": "o1",
                            "type": "html",
                            "value": "report_html",
                            "description": "Rapport HTML du pr\u00e9processing effectu\u00e9",
                            "ptype": "OUT"
                        },
                        {
                            "name": "o2",
                            "type": "json",
                            "value": "report_json",
                            "description": "Rapport JSON du pr\u00e9processing effectu\u00e9",
                            "ptype": "OUT"
                        },
                        {
                            "name": "o3",
                            "type": "fq.gz",
                            "value": "read_preprocessed",
                            "description": "Reads R1 pr\u00e9process\u00e9s",
                            "ptype": "OUT"
                        },
                        {
                            "name": "o4",
                            "type": "fq.gz",
                            "value": "read2_preprocessed",
                            "description": "Reads R2 pr\u00e9process\u00e9s",
                            "ptype": "OUT"
                        }
                    ],
                    "outservices2": [
                        {
                            "name": "o5",
                            "type": "link",
                            "value": "linkOut"
                        }
                    ],
                    "description": "A tool designed to provide fast all-in-one preprocessing for FastQ files.",
                    "version": "0.20.0",
                    "key": "3081109998",
                    "loc": "-340 260"
                },
                {
                    "name": "fastp_SE",
                    "text": "Fastp SE",
                    "size2": "130 110",
                    "category": "Tool",
                    "strokeWidth": 2,
                    "fill": "#3498db",
                    "inservices": [
                        {
                            "name": "i1",
                            "type": "reads",
                            "value": "read1",
                            "description": "",
                            "ptype": "IN"
                        }
                    ],
                    "outservices": [
                        {
                            "name": "o1",
                            "type": "html",
                            "value": "report_html",
                            "description": "Rapport HTML du pr\u00e9processing effectu\u00e9",
                            "ptype": "OUT"
                        },
                        {
                            "name": "o2",
                            "type": "json",
                            "value": "report_json",
                            "description": "Rapport JSON du pr\u00e9processing effectu\u00e9",
                            "ptype": "OUT"
                        },
                        {
                            "name": "o3",
                            "type": "fq.gz",
                            "value": "read",
                            "description": "Reads pr\u00e9process\u00e9s",
                            "ptype": "OUT"
                        }
                    ],
                    "outservices2": [
                        {
                            "name": "o4",
                            "type": "link",
                            "value": "linkOut"
                        }
                    ],
                    "description": "A tool designed to provide fast all-in-one preprocessing for FastQ files.",
                    "version": "0.20.0",
                    "key": "4361238426",
                    "loc": "-340 -80"
                },
                {
                    "name": "trimmomatic_PE",
                    "text": "Trimmomatic PE",
                    "size2": "155 135",
                    "category": "Tool",
                    "strokeWidth": 2,
                    "fill": "#3498db",
                    "inservices": [
                        {
                            "name": "i1",
                            "type": "reads",
                            "value": "read",
                            "description": "",
                            "ptype": "IN"
                        },
                        {
                            "name": "i2",
                            "type": "reads",
                            "value": "read2",
                            "description": "",
                            "ptype": "IN"
                        }
                    ],
                    "outservices": [
                        {
                            "name": "o1",
                            "type": "fq.gz",
                            "value": "readFP",
                            "description": "Reads forward paired",
                            "ptype": "OUT"
                        },
                        {
                            "name": "o2",
                            "type": "fq.gz",
                            "value": "readFU",
                            "description": "Reads forward unpaired",
                            "ptype": "OUT"
                        },
                        {
                            "name": "o3",
                            "type": "fq.gz",
                            "value": "readRP",
                            "description": "Reads reverse paired",
                            "ptype": "OUT"
                        },
                        {
                            "name": "o4",
                            "type": "fq.gz",
                            "value": "readRU",
                            "description": "Reads reverse unpaired",
                            "ptype": "OUT"
                        }
                    ],
                    "outservices2": [
                        {
                            "name": "o5",
                            "type": "link",
                            "value": "linkOut"
                        }
                    ],
                    "description": "A flexible read trimming tool for Illumina NGS data",
                    "version": "0.38",
                    "key": "5829873868",
                    "loc": "-150 100"
                },
                {
                    "name": "trimmomatic_SE",
                    "text": "Trimmomatic SE",
                    "size2": "155 60",
                    "category": "Tool",
                    "strokeWidth": 2,
                    "fill": "#3498db",
                    "inservices": [
                        {
                            "name": "i1",
                            "type": "reads",
                            "value": "read",
                            "description": "",
                            "ptype": "IN"
                        }
                    ],
                    "outservices": [
                        {
                            "name": "o1",
                            "type": "fq.gz",
                            "value": "read",
                            "description": "Reads trimmed",
                            "ptype": "OUT"
                        }
                    ],
                    "outservices2": [
                        {
                            "name": "o2",
                            "type": "link",
                            "value": "linkOut"
                        }
                    ],
                    "description": "A flexible read trimming tool for Illumina NGS data",
                    "version": "0.38",
                    "key": "1789674745",
                    "loc": "-160 -210"
                },
                {
                    "name": "flash",
                    "text": "Flash",
                    "size2": "125 160",
                    "category": "Tool",
                    "strokeWidth": 2,
                    "fill": "#3498db",
                    "inservices": [
                        {
                            "name": "i1",
                            "type": "reads",
                            "value": "read",
                            "description": "",
                            "ptype": "IN"
                        },
                        {
                            "name": "i2",
                            "type": "reads",
                            "value": "read2",
                            "description": "",
                            "ptype": "IN"
                        }
                    ],
                    "outservices": [
                        {
                            "name": "o1",
                            "type": [
                                "fastq",
                                "fq.gz"
                            ],
                            "value": "extendedFrags",
                            "description": "The merged reads.",
                            "ptype": "OUT"
                        },
                        {
                            "name": "o2",
                            "type": [
                                "fastq",
                                "fq.gz"
                            ],
                            "value": "notCombined_1",
                            "description": "Read 1 of mate pairs that were not merged.",
                            "ptype": "OUT"
                        },
                        {
                            "name": "o3",
                            "type": [
                                "fastq",
                                "fq.gz"
                            ],
                            "value": "notCombined_2",
                            "description": "Read 2 of mate pairs that were not merged.",
                            "ptype": "OUT"
                        },
                        {
                            "name": "o4",
                            "type": "hist",
                            "value": "hist",
                            "description": "Numeric histogram of merged read lengths.",
                            "ptype": "OUT"
                        },
                        {
                            "name": "o5",
                            "type": "histogram",
                            "value": "histogram",
                            "description": "Visual histogram of merged read lengths.",
                            "ptype": "OUT"
                        }
                    ],
                    "outservices2": [
                        {
                            "name": "o6",
                            "type": "link",
                            "value": "linkOut"
                        }
                    ],
                    "description": "FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments",
                    "version": "1.2.11",
                    "key": "2353637485",
                    "loc": "90 -110"
                },
                {
                    "name": "demultiplexing_astrid_cruaud",
                    "text": "Demultiplexing Astrid Cruaud",
                    "size2": "280 60",
                    "category": "Tool",
                    "strokeWidth": 2,
                    "fill": "#3498db",
                    "inservices": [
                        {
                            "name": "i1",
                            "type": "reads",
                            "value": "reads",
                            "description": "",
                            "ptype": "IN"
                        }
                    ],
                    "outservices": [
                        {
                            "name": "o1",
                            "type": "reads",
                            "value": "demultiplexed",
                            "description": "The demultiplexed reads.",
                            "ptype": "OUT"
                        }
                    ],
                    "outservices2": [
                        {
                            "name": "o2",
                            "type": "link",
                            "value": "linkOut"
                        }
                    ],
                    "description": "unknown",
                    "version": "unknown",
                    "key": "3923593754",
                    "loc": "370 -50"
                },
                {
                    "name": "velvet",
                    "text": "Velvet",
                    "size2": "125 110",
                    "category": "Tool",
                    "strokeWidth": 2,
                    "fill": "#3498db",
                    "inservices": [
                        {
                            "name": "i1",
                            "type": "reads",
                            "value": "read",
                            "description": "",
                            "ptype": "IN"
                        }
                    ],
                    "outservices": [
                        {
                            "name": "o1",
                            "type": "fasta",
                            "value": "contigs",
                            "description": "fasta file of contigs longer than twice hash length",
                            "ptype": "OUT"
                        },
                        {
                            "name": "o2",
                            "type": "txt",
                            "value": "stats",
                            "description": "stats file (tab-spaced) useful for determining appropriate coverage cutoff",
                            "ptype": "OUT"
                        },
                        {
                            "name": "o3",
                            "type": "LastGraph",
                            "value": "LastGraph",
                            "description": "special formatted file with all the information on the final graph",
                            "ptype": "OUT"
                        }
                    ],
                    "outservices2": [
                        {
                            "name": "o4",
                            "type": "link",
                            "value": "linkOut"
                        }
                    ],
                    "description": "Velvet is a de novo genomic assembler specially designed for short read sequencing technologies.",
                    "version": "1.2.10",
                    "key": "0948570832",
                    "loc": "170 120"
                },
                {
                    "name": "lastz",
                    "text": "Lastz",
                    "size2": "125 85",
                    "category": "Tool",
                    "strokeWidth": 2,
                    "fill": "#3498db",
                    "inservices": [
                        {
                            "name": "i1",
                            "type": "fasta",
                            "value": "reference_fasta",
                            "description": "",
                            "ptype": "IN"
                        },
                        {
                            "name": "i2",
                            "type": "fasta",
                            "value": "contigs",
                            "description": "",
                            "ptype": "IN"
                        }
                    ],
                    "outservices": [
                        {
                            "name": "o1",
                            "type": "sam",
                            "value": "align_on_ref",
                            "description": "Contigs mapping on reference",
                            "ptype": "OUT"
                        }
                    ],
                    "outservices2": [
                        {
                            "name": "o2",
                            "type": "link",
                            "value": "linkOut"
                        }
                    ],
                    "description": "A tool for aligning two DNA sequences, and inferring appropriate scoring parameters automatically",
                    "version": "1.04.03",
                    "key": "4680074655",
                    "loc": "430 200"
                },
                {
                    "name": "multiqc",
                    "text": "Multiqc",
                    "size2": "125 60",
                    "category": "Repport",
                    "strokeWidth": 2,
                    "fill": "#e67e22",
                    "inservices": [
                        {
                            "name": "i1",
                            "type": "*",
                            "value": "data",
                            "description": "",
                            "ptype": "IN"
                        }
                    ],
                    "outservices": [
                        {
                            "name": "o2",
                            "type": "html",
                            "value": "rapport",
                            "description": "Rapport",
                            "ptype": "OUT"
                        }
                    ],
                    "outservices2": [
                        {
                            "name": "o2",
                            "type": "link",
                            "value": "linkOut"
                        }
                    ],
                    "description": "Multiqc",
                    "version": "1",
                    "key": "9323328228",
                    "loc": "620 70"
                }
            ],
            "linkDataArray": [
                {
                    "from": -3,
                    "to": "4361238426",
                    "fromPort": "raw_reads",
                    "toPort": "read1",
                    "points": [
                        -491.94583320617676,
                        -206.9418333911896,
                        -473.94583320617676,
                        -206.9418333911896,
                        -451.4854166507721,
                        -206.9418333911896,
                        -451.4854166507721,
                        -78.60000000000001,
                        -429.02500009536743,
                        -78.60000000000001,
                        -419.02500009536743,
                        -78.60000000000001
                    ]
                },
                {
                    "from": -2,
                    "to": "3081109998",
                    "fromPort": "raw_reads",
                    "toPort": "read2",
                    "points": [
                        -501.94583320617676,
                        261.3,
                        -491.94583320617676,
                        261.3,
                        -460.4854166507721,
                        261.3,
                        -460.4854166507721,
                        271.94083304405217,
                        -429.02500009536743,
                        271.94083304405217,
                        -419.02500009536743,
                        271.94083304405217
                    ]
                },
                {
                    "from": -3,
                    "to": "3081109998",
                    "fromPort": "raw_reads",
                    "toPort": "read",
                    "points": [
                        -491.94583320617676,
                        -203.42550017356874,
                        -481.94583320617676,
                        -203.42550017356874,
                        -455.4854166507721,
                        -203.42550017356874,
                        -455.4854166507721,
                        248.3591669559479,
                        -429.02500009536743,
                        248.3591669559479,
                        -419.02500009536743,
                        248.3591669559479
                    ]
                },
                {
                    "from": -3,
                    "to": "5829873868",
                    "fromPort": "raw_reads",
                    "toPort": "read",
                    "points": [
                        -491.94583320617676,
                        -210.45816660881042,
                        -465.94583320617676,
                        -210.45816660881042,
                        -465.94583320617676,
                        -210.45816660881042,
                        -465.94583320617676,
                        88.35916695594788,
                        -251.52500009536743,
                        88.35916695594788,
                        -241.52500009536743,
                        88.35916695594788
                    ]
                },
                {
                    "from": -3,
                    "to": "1789674745",
                    "fromPort": "raw_reads",
                    "toPort": "read",
                    "points": [
                        -491.94583320617676,
                        -213.97449982643127,
                        -457.94583320617676,
                        -213.97449982643127,
                        -282.31875014305115,
                        -213.97449982643127,
                        -282.31875014305115,
                        -206.10000000000002,
                        -106.69166707992554,
                        -206.10000000000002,
                        -96.69166707992554,
                        -206.10000000000002
                    ]
                },
                {
                    "from": -2,
                    "to": "5829873868",
                    "fromPort": "raw_reads",
                    "toPort": "read2",
                    "points": [
                        -501.94583320617676,
                        258.3697223186493,
                        -491.94583320617676,
                        258.3697223186493,
                        -491.94583320617676,
                        258.3697223186493,
                        -491.94583320617676,
                        111.94083304405213,
                        -251.52500009536743,
                        111.94083304405213,
                        -241.52500009536743,
                        111.94083304405213
                    ]
                },
                {
                    "from": "1789674745",
                    "to": "2353637485",
                    "fromPort": "read",
                    "toPort": "read",
                    "points": [
                        -68.47499990463257,
                        -206.10000000000002,
                        -58.47499990463257,
                        -206.10000000000002,
                        -27.5,
                        -206.10000000000002,
                        -27.5,
                        -125.82111072540282,
                        3.4749999046325684,
                        -125.82111072540282,
                        13.474999904632568,
                        -125.82111072540282
                    ]
                },
                {
                    "from": "5829873868",
                    "to": "2353637485",
                    "fromPort": "readFP",
                    "toPort": "read",
                    "points": [
                        -58.47499990463257,
                        64.77750086784363,
                        -48.47499990463257,
                        64.77750086784363,
                        -22.5,
                        64.77750086784363,
                        -22.5,
                        -119.96055536270141,
                        3.4749999046325684,
                        -119.96055536270141,
                        13.474999904632568,
                        -119.96055536270141
                    ]
                },
                {
                    "from": "5829873868",
                    "to": "2353637485",
                    "fromPort": "readFU",
                    "toPort": "read2",
                    "points": [
                        -58.47499990463257,
                        88.35916695594788,
                        -48.47499990463257,
                        88.35916695594788,
                        -22.5,
                        88.35916695594788,
                        -22.5,
                        -99.30916695594787,
                        3.4749999046325684,
                        -99.30916695594787,
                        13.474999904632568,
                        -99.30916695594787
                    ]
                },
                {
                    "from": "2353637485",
                    "to": "3923593754",
                    "fromPort": "extendedFrags",
                    "toPort": "reads",
                    "points": [
                        166.52500009536743,
                        -158.2633321762085,
                        176.52500009536743,
                        -158.2633321762085,
                        191.25,
                        -158.2633321762085,
                        191.25,
                        -46.099999999999994,
                        205.97499990463257,
                        -46.099999999999994,
                        215.97499990463257,
                        -46.099999999999994
                    ]
                },
                {
                    "from": "3923593754",
                    "to": "0948570832",
                    "fromPort": "demultiplexed",
                    "toPort": "read",
                    "points": [
                        524.0250000953674,
                        -46.099999999999994,
                        534.0250000953674,
                        -46.099999999999994,
                        534.0250000953674,
                        22.5,
                        83.47499990463257,
                        22.5,
                        83.47499990463257,
                        121.39999999999999,
                        93.47499990463257,
                        121.39999999999999
                    ]
                },
                {
                    "from": "0948570832",
                    "to": "4680074655",
                    "fromPort": "contigs",
                    "toPort": "reference_fasta",
                    "points": [
                        246.52500009536743,
                        97.81833391189575,
                        256.52500009536743,
                        97.81833391189575,
                        300,
                        97.81833391189575,
                        300,
                        190.8591669559479,
                        343.47499990463257,
                        190.8591669559479,
                        353.47499990463257,
                        190.8591669559479
                    ]
                },
                {
                    "from": "4680074655",
                    "to": "9323328228",
                    "fromPort": "align_on_ref",
                    "toPort": "data",
                    "points": [
                        506.52500009536743,
                        202.64999999999998,
                        516.5250000953674,
                        202.64999999999998,
                        525,
                        202.64999999999998,
                        525,
                        73.9,
                        533.4749999046326,
                        73.9,
                        543.4749999046326,
                        73.9
                    ]
                }
            ],
            "version": 2
        },
        "yaml": "{\n  name: Capture_UCE,\n  docker_name: capture_uce,\n  description: \"\",\n  version: \"0.0.1\",\n  author: \"MBB\",\n  input: raw_reads,\n  steps:\n    [\n      { title: \"Quality control\", name: \"quality_control\", tools: [fastqc], default: \"fastqc\" },\n      { title: \"Quality filtering and adapter trimming\", name: \"qcfilter_adaptertrim\", tools: [trimmomatic], default: \"trimmomatic\" },\n      { title: \"Merge of overlapping reads\", name: \"merge_overlapps\", tools: [flash], default: \"flash\" },\n      { title: \"Demultiplexing\", name: \"demultiplexing\", tools: [demultiplexing_astrid_cruaud], default: \"demultiplexing_astrid_cruaud\" },\n      { title: \"Assembling\", name: \"assembling\", tools: [velvet], default: \"velvet\" },\n      { title: \"Contigs map to UCEs references\", name: \"contigmaptouce\", tools: [lastz], default: \"lastz\" },\n      { title: \"Mapping check before filter\", name: \"mapping_check_bf\", tools: [samtools_stats], default: \"samtools_stats\" }, # Check lastz sams before and after filtering\n      { title: \"Mapping check after filter\", name: \"mapping_check_af\", tools: [samtools_stats], default: \"samtools_stats\" }, # Check lastz sams before and after filtering\n      { title: \"Convert to phylip\", name: \"convert_to_phylip\", tools: [sam_to_phylip], default: \"sam_to_phylip\" },\n      #{ title: \"Selection of UCEs\", name: \"selectuces\", tools: [TODO], default: },\n    ],\n  options:\n    [\n      {\n        name: \"results_dir\",\n        type: \"output_dir\",\n        value: \"\/Results\",\n        label: \"Results directory: \",\n        volumes:  [Results: \"\/Results\"]\n      },\n    ],\n    steps_in: [\n      { step_name: quality_control, tool_name: fastqc, rule_name: fastqc_PE, \n        params: [ \n          {input_name: read, origin_step: \"\", origin_command: raw_reads, origin_name: read },\n          {input_name: read2, origin_step: \"\", origin_command: raw_reads, origin_name: read2 }\n        ]\n      },\n\n      { step_name: qcfilter_adaptertrim, tool_name: trimmomatic, rule_name: trimmomatic_PE, \n        params: [ \n          {input_name: read, origin_step: \"\", origin_command: raw_reads, origin_name: read },\n          {input_name: read2, origin_step: \"\", origin_command: raw_reads, origin_name: read2 }\n        ]\n      },\n\n      { step_name: merge_overlapps, tool_name: flash, rule_name: flash, \n        params: [ \n          {input_name: read, origin_step: \"qcfilter_adaptertrim\", origin_command: trimmomatic_PE, origin_name: readFP },\n          {input_name: read2, origin_step: \"qcfilter_adaptertrim\", origin_command: trimmomatic_PE, origin_name: readRP }\n        ]\n      },\n\n      { step_name: demultiplexing, tool_name: demultiplexing_astrid_cruaud, rule_name: demultiplexing_astrid_cruaud, \n        params: [ \n          {input_name: extended_frags, origin_step: \"merge_overlapps\" , origin_command: flash, origin_name: extendedFrags }\n        ]\n      },\n\n      { step_name: assembling, tool_name: velvet, rule_name: velvet, \n        params: [ \n          {input_name: merged_reads, origin_step: \"demultiplexing\", origin_command: demultiplexing_astrid_cruaud, origin_name: demultiplexed }\n        ]\n      },\n\n      { step_name: contigmaptouce, tool_name: lastz, rule_name: lastz, \n        params: [ \n          {input_name: contigs, origin_step: \"assembling\", origin_command: velvet, origin_name: contigs }\n        ]\n      },\n\n      { step_name: mapping_check_bf, tool_name: samtools_stats, rule_name: samtools_stats, \n        params: [ \n          {input_name: \"bam\", origin_step: \"contigmaptouce\", origin_command: lastz, origin_name: align_on_ref }\n        ]\n      },\n\n      { step_name: mapping_check_af, tool_name: samtools_stats, rule_name: samtools_stats, \n        params: [ \n          {input_name: \"bam\", origin_step: \"contigmaptouce\", origin_command: lastz, origin_name: filtered }\n        ]\n      },\n\n      { step_name: convert_to_phylip, tool_name: sam_to_phylip, rule_name: sam_to_phylip, \n        params: [ \n          {input_name: \"sams\", origin_step: \"contigmaptouce\", origin_command: lastz, origin_name: filtered }\n        ]\n      },\n    ],\n}\n"
    }
]