[
    {
        "name": "Variant_calling_benchmark",
        "docker_name": "variantcallingbenchmark",
        "description": null,
        "version": "0.0.1",
        "author": "MBB",
        "input": "raw_reads",
        "steps": [
            {
                "title": "Preprocessing",
                "name": "preprocess",
                "tools": [
                    "fastp",
                    "null"
                ],
                "default": "fastp"
            },
            {
                "title": "Mapping",
                "name": "mapping",
                "tools": [
                    "bwa",
                    "bowtie"
                ],
                "default": "bwa"
            },
            {
                "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",
                    "null"
                ],
                "default": "bcftools_mpileup"
            },
            {
                "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": "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"
            }
        ],
        "params_equals": [
            {
                "param_A": "genome_fasta",
                "param_B": "bwa_index_genome_fasta"
            },
            {
                "param_A": "genome_fasta",
                "param_B": "bowtie_index_genome_fasta"
            },
            {
                "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"
            }
        ],
        "git": "",
        "json": "",
        "yaml": "{\n  name: Variant_calling_benchmark,\n  docker_name: variantcallingbenchmark,\n  description: ,\n  version: \"0.0.1\",\n  author: \"MBB\",\n  input: raw_reads,\n  steps:\n    [\n        { title: Preprocessing, name: preprocess, tools: [fastp, \"null\"], default: fastp },\n        { title: Mapping, name: mapping, tools: [bwa, bowtie], default: bwa },\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, \"null\"], default: bcftools_mpileup },\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: 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    params_equals: [\n      { param_A: genome_fasta, param_B: bwa_index_genome_fasta },\n      { param_A: genome_fasta, param_B: bowtie_index_genome_fasta },\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    ],\n}\n"
    }
]