annotate Galaxy-Workflow-MMuFF.ga @ 5:60a6f2d92058

Adding Galaxy-Workflow-MMuFF.ga (version 1.4 updated for SnpEff v3.2 and snpeff_cds_report v1.2)

{
    "a_galaxy_workflow": "true", 
    "annotation": "", 
    "format-version": "0.1", 
    "name": "MMuFF_Human_v1.4", 
    "steps": {
        "0": {
            "annotation": "Human RNA-seq paired reads left mates", 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "Human RNA-seq paired reads left mates", 
                    "name": "Forward reads fastq"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 240, 
                "top": 314
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"Forward reads fastq\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "1": {
            "annotation": "Human RNA-seq paired reads right mates", 
            "id": 1, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "Human RNA-seq paired reads right mates", 
                    "name": "Reverse reads fastq"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 249, 
                "top": 410
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"Reverse reads fastq\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "2": {
            "annotation": "Known SNPs  - dbSNP.vcf", 
            "id": 2, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "Known SNPs  - dbSNP.vcf", 
                    "name": "VCF file of known variants (dbSNP)"
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 2362, 
                "top": 745
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"VCF file of known variants (dbSNP)\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "3": {
            "annotation": "These are locations other than those in dbSNP.  This could include variants from the subject normal tissue.  \nThe ID will be used to annotate the Variants dataset, and then can be filtered out.  There needs to be at least one  entry for  each chromosome: (M,1,2,...,X,Y)", 
            "id": 3, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "These are locations other than those in dbSNP.  This could include variants from the subject normal tissue.  \nThe ID will be used to annotate the Variants dataset, and then can be filtered out.  There needs to be at least one  entry for  each chromosome: (M,1,2,...,X,Y)", 
                    "name": "VCF file of additional known variants "
                }
            ], 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 4388, 
                "top": 576
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"VCF file of additional known variants \"}", 
            "tool_version": null, 
            "type": "data_input", 
            "user_outputs": []
        }, 
        "4": {
            "annotation": "Convert quality scores to sanger scale", 
            "id": 4, 
            "input_connections": {
                "input_file": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool FASTQ Groomer", 
                    "name": "input_type"
                }
            ], 
            "name": "FASTQ Groomer", 
            "outputs": [
                {
                    "name": "output_file", 
                    "type": "fastqsanger"
                }
            ], 
            "position": {
                "left": 510, 
                "top": 291
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "fastq_groomer", 
            "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/?.len\\\"\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", 
            "tool_version": "1.0.4", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "5": {
            "annotation": "Convert quality scores to sanger scale", 
            "id": 5, 
            "input_connections": {
                "input_file": {
                    "id": 1, 
                    "output_name": "output"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool FASTQ Groomer", 
                    "name": "input_type"
                }
            ], 
            "name": "FASTQ Groomer", 
            "outputs": [
                {
                    "name": "output_file", 
                    "type": "fastqsanger"
                }
            ], 
            "position": {
                "left": 505, 
                "top": 431
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "fastq_groomer", 
            "tool_state": "{\"__page__\": 0, \"input_type\": \"{\\\"__class__\\\": \\\"RuntimeValue\\\"}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/?.len\\\"\", \"options_type\": \"{\\\"options_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"input_file\": \"null\"}", 
            "tool_version": "1.0.4", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "6": {
            "annotation": "Map paired reads to reference genome", 
            "id": 6, 
            "input_connections": {
                "input1": {
                    "id": 4, 
                    "output_name": "output_file"
                }, 
                "singlePaired|input2": {
                    "id": 5, 
                    "output_name": "output_file"
                }
            }, 
            "inputs": [
                {
                    "description": "runtime parameter for tool Tophat for Illumina", 
                    "name": "singlePaired"
                }
            ], 
            "name": "Tophat for Illumina", 
            "outputs": [
                {
                    "name": "insertions", 
                    "type": "bed"
                }, 
                {
                    "name": "deletions", 
                    "type": "bed"
                }, 
                {
                    "name": "junctions", 
                    "type": "bed"
                }, 
                {
                    "name": "accepted_hits", 
                    "type": "bam"
                }
            ], 
            "position": {
                "left": 884, 
                "top": 332
            }, 
            "post_job_actions": {
                "HideDatasetActiondeletions": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "deletions"
                }, 
                "HideDatasetActioninsertions": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "insertions"
                }, 
                "HideDatasetActionjunctions": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "junctions"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "tophat", 
            "tool_state": "{\"__page__\": 0, \"refGenomeSource\": \"{\\\"genomeSource\\\": \\\"indexed\\\", \\\"index\\\": \\\"hg19_canonical\\\", \\\"__current_case__\\\": 0}\", \"input1\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/?.len\\\"\", \"singlePaired\": \"{\\\"input2\\\": null, \\\"sPaired\\\": \\\"paired\\\", \\\"pParams\\\": {\\\"library_type\\\": \\\"fr-unstranded\\\", \\\"closure_search\\\": {\\\"use_search\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"__current_case__\\\": 1, \\\"indel_search\\\": {\\\"max_insertion_length\\\": \\\"3\\\", \\\"max_deletion_length\\\": \\\"3\\\", \\\"__current_case__\\\": 1, \\\"allow_indel_search\\\": \\\"Yes\\\"}, \\\"seg_length\\\": \\\"25\\\", \\\"max_intron_length\\\": \\\"500000\\\", \\\"pSettingsType\\\": \\\"full\\\", \\\"min_intron_length\\\": \\\"70\\\", \\\"microexon_search\\\": \\\"No\\\", \\\"min_segment_intron\\\": \\\"50\\\", \\\"max_multihits\\\": \\\"1\\\", \\\"coverage_search\\\": {\\\"use_search\\\": \\\"Yes\\\", \\\"max_coverage_intron\\\": \\\"20000\\\", \\\"__current_case__\\\": 0, \\\"min_coverage_intron\\\": \\\"50\\\"}, \\\"splice_mismatches\\\": \\\"0\\\", \\\"anchor_length\\\": \\\"8\\\", \\\"mate_std_dev\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}, \\\"own_junctions\\\": {\\\"use_junctions\\\": \\\"No\\\", \\\"__current_case__\\\": 1}, \\\"seg_mismatches\\\": \\\"2\\\", \\\"initial_read_mismatches\\\": \\\"2\\\", \\\"max_segment_intron\\\": \\\"500000\\\"}, \\\"__current_case__\\\": 1, \\\"mate_inner_distance\\\": {\\\"__class__\\\": \\\"RuntimeValue\\\"}}\"}", 
            "tool_version": "1.5.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "7": {
            "annotation": "Keep only unique mappings - MAPQ of 255\n(255 is the value tophat uses to indicate that reads are uniquely mapped in the genome)", 
            "id": 7, 
            "input_connections": {
                "input1": {
                    "id": 6, 
                    "output_name": "accepted_hits"
                }
            }, 
            "inputs": [], 
            "name": "Filter SAM or BAM", 
            "outputs": [
                {
                    "name": "output1", 
                    "type": "sam"
                }
            ], 
            "position": {
                "left": 1154, 
                "top": 366
            }, 
            "post_job_actions": {
                "HideDatasetActionoutput1": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output1"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "samtools_filter", 
            "tool_state": "{\"__page__\": 0, \"bed_file\": \"null\", \"input1\": \"null\", \"read_group\": \"\\\"\\\"\", \"library\": \"\\\"\\\"\", \"regions\": \"\\\"\\\"\", \"header\": \"\\\"-h\\\"\", \"flag\": \"{\\\"filter\\\": \\\"no\\\", \\\"__current_case__\\\": 0}\", \"mapq\": \"\\\"255\\\"\"}", 
            "tool_version": "1.1.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "8": {
            "annotation": "", 
            "id": 8, 
            "input_connections": {
                "input1": {
                    "id": 7, 
                    "output_name": "output1"
                }
            }, 
            "inputs": [], 
            "name": "flagstat", 
            "outputs": [
                {
                    "name": "output1", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 1505, 
                "top": 323
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "samtools_flagstat", 
            "tool_state": "{\"__page__\": 0, \"input1\": \"null\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", 
            "tool_version": "1.0.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "9": {
            "annotation": "Add Read Group info required by GATK tools", 
            "id": 9, 
            "input_connections": {
                "inputFile": {
                    "id": 7, 
                    "output_name": "output1"
                }
            }, 
            "inputs": [], 
            "name": "Add or Replace Groups", 
            "outputs": [
                {
                    "name": "outFile", 
                    "type": "bam"
                }
            ], 
            "position": {
                "left": 1506, 
                "top": 503
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ARRG/1.56.0", 
            "tool_state": "{\"rgpl\": \"\\\"ILLUMINA\\\"\", \"outputFormat\": \"\\\"True\\\"\", \"__page__\": 0, \"rgsm\": \"\\\"1\\\"\", \"readGroupOpts\": \"{\\\"rgOpts\\\": \\\"preSet\\\", \\\"__current_case__\\\": 0}\", \"rgid\": \"\\\"1\\\"\", \"rgpu\": \"\\\"1.5\\\"\", \"rglb\": \"\\\"1\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"inputFile\": \"null\"}", 
            "tool_version": "1.56.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "10": {
            "annotation": "Synchronize paired reads", 
            "id": 10, 
            "input_connections": {
                "input_file": {
                    "id": 9, 
                    "output_name": "outFile"
                }
            }, 
            "inputs": [], 
            "name": "Paired Read Mate Fixer", 
            "outputs": [
                {
                    "name": "out_file", 
                    "type": "bam"
                }
            ], 
            "position": {
                "left": 1841, 
                "top": 375
            }, 
            "post_job_actions": {
                "HideDatasetActionout_file": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "out_file"
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            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicFixMate/1.56.0", 
            "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"True\\\"\", \"input_file\": \"null\", \"out_prefix\": \"\\\"Fix Mate\\\"\", \"sortOrder\": \"\\\"coordinate\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", 
            "tool_version": "1.56.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "11": {
            "annotation": "Remove duplicate reads", 
            "id": 11, 
            "input_connections": {
                "input_file": {
                    "id": 10, 
                    "output_name": "out_file"
                }
            }, 
            "inputs": [], 
            "name": "Mark Duplicate reads", 
            "outputs": [
                {
                    "name": "out_file", 
                    "type": "bam"
                }, 
                {
                    "name": "html_file", 
                    "type": "html"
                }
            ], 
            "position": {
                "left": 2086, 
                "top": 360
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0", 
            "tool_state": "{\"remDups\": \"\\\"True\\\"\", \"assumeSorted\": \"\\\"True\\\"\", \"input_file\": \"null\", \"readRegex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*\\\"\", \"__page__\": 0, \"out_prefix\": \"\\\"Dupes Marked\\\"\", \"optDupeDist\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", 
            "tool_version": "1.56.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "12": {
            "annotation": "Reorder BAM for GATK tools", 
            "id": 12, 
            "input_connections": {
                "inputFile": {
                    "id": 11, 
                    "output_name": "out_file"
                }
            }, 
            "inputs": [], 
            "name": "Reorder SAM/BAM", 
            "outputs": [
                {
                    "name": "outFile", 
                    "type": "bam"
                }
            ], 
            "position": {
                "left": 2401, 
                "top": 332
            }, 
            "post_job_actions": {}, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_ReorderSam/1.56.0", 
            "tool_state": "{\"__page__\": 0, \"outputFormat\": \"\\\"True\\\"\", \"allowContigLenDiscord\": \"\\\"False\\\"\", \"allowIncDictConcord\": \"\\\"False\\\"\", \"source\": \"{\\\"indexSource\\\": \\\"built-in\\\", \\\"ref\\\": \\\"hg19_canonical\\\", \\\"__current_case__\\\": 0}\", \"inputFile\": \"null\"}", 
            "tool_version": "1.56.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "13": {
            "annotation": "", 
            "id": 13, 
            "input_connections": {
                "reference_source|input_bam": {
                    "id": 12, 
                    "output_name": "outFile"
                }, 
                "rod_bind_0|rod_bind_type|input_rod": {
                    "id": 2, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "name": "Realigner Target Creator", 
            "outputs": [
                {
                    "name": "output_interval", 
                    "type": "gatk_interval"
                }, 
                {
                    "name": "output_log", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 2565, 
                "top": 518
            }, 
            "post_job_actions": {
                "HideDatasetActionoutput_log": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output_log"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "gatk_realigner_target_creator", 
            "tool_state": "{\"__page__\": 0, \"gatk_param_type\": \"{\\\"gatk_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"analysis_param_type\": \"{\\\"analysis_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"hg19_canonical\\\"}, \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bam\\\": null, \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"rod_bind\": \"[{\\\"__index__\\\": 0, \\\"rod_bind_type\\\": {\\\"rod_bind_type_selector\\\": \\\"dbsnp\\\", \\\"__current_case__\\\": 0, \\\"input_rod\\\": null}}]\"}", 
            "tool_version": "0.0.4", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "14": {
            "annotation": "Perform local realignments for indels", 
            "id": 14, 
            "input_connections": {
                "reference_source|input_bam": {
                    "id": 12, 
                    "output_name": "outFile"
                }, 
                "target_intervals": {
                    "id": 13, 
                    "output_name": "output_interval"
                }
            }, 
            "inputs": [], 
            "name": "Indel Realigner", 
            "outputs": [
                {
                    "name": "output_bam", 
                    "type": "bam"
                }, 
                {
                    "name": "output_log", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 2811, 
                "top": 351
            }, 
            "post_job_actions": {
                "HideDatasetActionoutput_log": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output_log"
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            }, 
            "tool_errors": null, 
            "tool_id": "gatk_indel_realigner", 
            "tool_state": "{\"__page__\": 0, \"knowns_only\": \"\\\"False\\\"\", \"gatk_param_type\": \"{\\\"gatk_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"lod_threshold\": \"\\\"5.0\\\"\", \"analysis_param_type\": \"{\\\"analysis_param_type_selector\\\": \\\"basic\\\", \\\"__current_case__\\\": 0}\", \"target_intervals\": \"null\", \"reference_source\": \"{\\\"ref_file\\\": {\\\"__class__\\\": \\\"UnvalidatedValue\\\", \\\"value\\\": \\\"hg19_canonical\\\"}, \\\"reference_source_selector\\\": \\\"cached\\\", \\\"input_bam\\\": null, \\\"__current_case__\\\": 0}\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\", \"rod_bind\": \"[]\"}", 
            "tool_version": "0.0.6", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "15": {
            "annotation": "Check again for duplicate reads and eliminate", 
            "id": 15, 
            "input_connections": {
                "input_file": {
                    "id": 14, 
                    "output_name": "output_bam"
                }
            }, 
            "inputs": [], 
            "name": "Mark Duplicate reads", 
            "outputs": [
                {
                    "name": "out_file", 
                    "type": "bam"
                }, 
                {
                    "name": "html_file", 
                    "type": "html"
                }
            ], 
            "position": {
                "left": 3174, 
                "top": 318
            }, 
            "post_job_actions": {
                "HideDatasetActionhtml_file": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "html_file"
                }, 
                "HideDatasetActionout_file": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "out_file"
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            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/picard/rgPicardMarkDups/1.56.0", 
            "tool_state": "{\"remDups\": \"\\\"True\\\"\", \"assumeSorted\": \"\\\"True\\\"\", \"input_file\": \"null\", \"readRegex\": \"\\\"[a-zA-Z0-9]+:[0-9]:([0-9]+):([0-9]+):([0-9]+).*\\\"\", \"__page__\": 0, \"out_prefix\": \"\\\"Dupes Marked\\\"\", \"optDupeDist\": \"\\\"100\\\"\", \"chromInfo\": \"\\\"/website/galaxy.msi.umn.edu/PRODUCTION/tool-data/shared/ucsc/chrom/hg19_canonical.len\\\"\"}", 
            "tool_version": "1.56.0", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "16": {
            "annotation": "Determine base calls at each position", 
            "id": 16, 
            "input_connections": {
                "reference_source|input_bams_0|input_bam": {
                    "id": 15, 
                    "output_name": "out_file"
                }
            }, 
            "inputs": [], 
            "name": "MPileup", 
            "outputs": [
                {
                    "name": "output_mpileup", 
                    "type": "pileup"
                }, 
                {
                    "name": "output_log", 
                    "type": "txt"
                }
            ], 
            "position": {
                "left": 3554, 
                "top": 292
            }, 
            "post_job_actions": {
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                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output_log"
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                "HideDatasetActionoutput_mpileup": {
                    "action_arguments": {}, 
                    "action_type": "HideDatasetAction", 
                    "output_name": "output_mpileup"
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            }, 
            "tool_errors": null, 
            "tool_id": "samtools_mpileup", 
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            "tool_version": "0.0.1", 
            "type": "tool", 
            "user_outputs": []
        }, 
        "17": {
            "annotation": "Minimum Base Quality: 30\nMinimum Coverage Depth: 5\nMinimum Frequency of a Specific Allele:  .33\nLeave VCF_ID blank for tumor sample", 
            "id": 17, 
            "input_connections": {
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