[
    {
        "name": "Variant_calling_benchmark_From_bam",
        "docker_name": "variantcalling_benchmark_frombam",
        "description": null,
        "version": "0.0.1",
        "author": "MBB",
        "input": "raw_bams",
        "steps": [
            {
                "title": "Mark Duplicates",
                "name": "mark_duplicates",
                "tools": [
                    "Picard_MarkDuplicates",
                    "null"
                ],
                "default": "Picard_MarkDuplicates"
            },
            {
                "title": "Indel Realign",
                "name": "indel_realign",
                "tools": [
                    "gatk_IndelRealigner",
                    "null"
                ],
                "default": "gatk_IndelRealigner"
            },
            {
                "title": "Variant calling gatk",
                "name": "variant_calling_gatk",
                "tools": [
                    "gatk_haplotype_caller",
                    "null"
                ],
                "default": "gatk_haplotype_caller"
            },
            {
                "title": "Variant calling bcftools",
                "name": "variant_calling_bcftools",
                "tools": [
                    "bcftools_mpileup_and_call",
                    "null"
                ],
                "default": "bcftools_mpileup_and_call"
            },
            {
                "title": "Variant calling deepvariant",
                "name": "variant_calling_deepvariant",
                "tools": [
                    "deep_variant",
                    "null"
                ],
                "default": "deep_variant"
            },
            {
                "title": "Variant calling freebayes",
                "name": "variant_calling_freebayes",
                "tools": [
                    "freebayes",
                    "null"
                ],
                "default": "freebayes"
            },
            {
                "title": "Variant calling octopus",
                "name": "variant_calling_octopus",
                "tools": [
                    "octopus",
                    "null"
                ],
                "default": "octopus"
            },
            {
                "title": "Compare VCFs",
                "name": "compare_vcfs",
                "tools": [
                    "compare_vcfs_isec",
                    "null"
                ],
                "default": "compare_vcfs_isec"
            },
            {
                "title": "Plot VCFs",
                "name": "plot_vcfs",
                "tools": [
                    "vcfparser",
                    "vcf_plot_dv",
                    "null"
                ],
                "default": "vcfparser"
            }
        ],
        "options": [
            {
                "name": "results_dir",
                "type": "output_dir",
                "value": "\/Results",
                "label": "Results directory: ",
                "volumes": [
                    {
                        "Results": "\/Results"
                    }
                ]
            },
            {
                "name": "genome_fasta",
                "type": "input_file",
                "value": "",
                "label": "Path to reference genome fasta file"
            }
        ],
        "steps_in": [
            {
                "step_name": "mark_duplicates",
                "tool_name": "Picard_MarkDuplicates",
                "rule_name": "Picard_MarkDuplicates",
                "params": [
                    {
                        "input_name": "bam",
                        "origin_command": "raw_bams",
                        "origin_name": "bam"
                    }
                ]
            },
            {
                "step_name": "mark_duplicates",
                "tool_name": "null",
                "rule_name": "null",
                "params": [
                    {
                        "input_name": "bam",
                        "origin_command": "raw_bams",
                        "origin_name": "bam"
                    }
                ]
            },
            {
                "step_name": "indel_realign",
                "tool_name": "gatk_IndelRealigner",
                "rule_name": "gatk_IndelRealigner",
                "params": [
                    {
                        "input_name": "bam",
                        "origin_command": "Picard_MarkDuplicates",
                        "origin_name": "bam"
                    }
                ]
            },
            {
                "step_name": "indel_realign",
                "tool_name": "gatk_IndelRealigner",
                "rule_name": "gatk_IndelRealigner",
                "params": [
                    {
                        "input_name": "bam",
                        "origin_command": "mark_duplicates_null",
                        "origin_name": "bam"
                    }
                ]
            }
        ],
        "params_equals": [
            {
                "param_A": "genome_fasta",
                "param_B": "gatk_IndelRealigner_genome_fasta"
            },
            {
                "param_A": "genome_fasta",
                "param_B": "gatk_haplotype_caller_genome_fasta"
            },
            {
                "param_A": "genome_fasta",
                "param_B": "bcftools_mpileup_and_call_genome_fasta"
            },
            {
                "param_A": "genome_fasta",
                "param_B": "deep_variant_genome_fasta"
            },
            {
                "param_A": "genome_fasta",
                "param_B": "freebayes_genome_fasta"
            },
            {
                "param_A": "genome_fasta",
                "param_B": "octopus_genome_fasta"
            }
        ],
        "stop_cases": {
            "max_readGroups": 1
        },
        "git": "",
        "json": "",
        "yaml": "{\n  name: Variant_calling_benchmark_From_bam,\n  docker_name: variantcalling_benchmark_frombam,\n  description: ,\n  version: \"0.0.1\",\n  author: \"MBB\",\n  input: raw_bams,\n  steps:\n    [\n      { title: Mark Duplicates, name: mark_duplicates, tools: [Picard_MarkDuplicates, \"null\"], default: Picard_MarkDuplicates },\n      { title: Indel Realign, name: indel_realign, tools: [gatk_IndelRealigner, \"null\"], default: gatk_IndelRealigner },\n      { title: Variant calling gatk, name: variant_calling_gatk, tools: [gatk_haplotype_caller, \"null\"], default: gatk_haplotype_caller },\n      { title: Variant calling bcftools, name: variant_calling_bcftools, tools: [bcftools_mpileup_and_call, \"null\"], default: bcftools_mpileup_and_call },\n      { title: Variant calling deepvariant, name: variant_calling_deepvariant, tools: [deep_variant, \"null\"], default: deep_variant },\n      { title: Variant calling freebayes, name: variant_calling_freebayes, tools: [freebayes, \"null\"], default: freebayes },\n      { title: Variant calling octopus, name: variant_calling_octopus, tools: [octopus, \"null\"], default: octopus },\n      { title: Compare VCFs, name: compare_vcfs, tools: [compare_vcfs_isec, \"null\"], default: compare_vcfs_isec },\n      { title: Plot VCFs, name: plot_vcfs, tools: [vcfparser, vcf_plot_dv, \"null\"], default: vcfparser }\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        name: genome_fasta,\n        type: input_file,\n        value: \"\",\n        label: \"Path to reference genome fasta file\",\n      },\n    ],\n    steps_in: [\n      { step_name: mark_duplicates, tool_name: Picard_MarkDuplicates, rule_name: Picard_MarkDuplicates, \n        params: [ \n          {input_name: bam, origin_command: raw_bams, origin_name: bam }\n        ]\n      },\n      { step_name: mark_duplicates, tool_name: \"null\", rule_name: \"null\", \n        params: [ \n          {input_name: bam, origin_command: raw_bams, origin_name: bam }\n        ]\n      },\n\n      { step_name: indel_realign, tool_name: \"gatk_IndelRealigner\", rule_name: \"gatk_IndelRealigner\", \n        params: [ \n          {input_name: bam, origin_command: Picard_MarkDuplicates, origin_name: bam }\n        ]\n      },\n      { step_name: indel_realign, tool_name: \"gatk_IndelRealigner\", rule_name: \"gatk_IndelRealigner\", \n        params: [ \n          {input_name: bam, origin_command: \"mark_duplicates_null\", origin_name: bam }\n        ]\n      },\n    ],\n    params_equals: [\n      { param_A: genome_fasta, param_B: gatk_IndelRealigner_genome_fasta },\n      { param_A: genome_fasta, param_B: gatk_haplotype_caller_genome_fasta },\n      { param_A: genome_fasta, param_B: bcftools_mpileup_and_call_genome_fasta },\n      { param_A: genome_fasta, param_B: deep_variant_genome_fasta },\n      { param_A: genome_fasta, param_B: freebayes_genome_fasta },\n      { param_A: genome_fasta, param_B: octopus_genome_fasta },\n    ],\n    stop_cases: {\n      max_readGroups: 1\n    }\n}\n"
    }
]