view Galaxy-Workflow-Phenix_workflow.ga @ 14:2e5a83c0f78f draft

Uploaded

{
    "a_galaxy_workflow": "true", 
    "annotation": "", 
    "format-version": "0.1", 
    "name": "Phenix workflow", 
    "steps": {
        "0": {
            "annotation": "", 
            "content_id": null, 
            "id": 0, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "Reference fasta"
                }
            ], 
            "label": null, 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 200, 
                "top": 128
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"Reference fasta\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "uuid": "2f18889e-5448-460b-8167-e04125fd51cf", 
            "workflow_outputs": []
        }, 
        "1": {
            "annotation": "", 
            "content_id": null, 
            "id": 1, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "R1 fastq"
                }
            ], 
            "label": null, 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 189, 
                "top": 296
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"R1 fastq\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "uuid": "5c634897-4a61-4a99-87c6-d4e23404af6c", 
            "workflow_outputs": []
        }, 
        "2": {
            "annotation": "", 
            "content_id": null, 
            "id": 2, 
            "input_connections": {}, 
            "inputs": [
                {
                    "description": "", 
                    "name": "R2 fastqs"
                }
            ], 
            "label": null, 
            "name": "Input dataset", 
            "outputs": [], 
            "position": {
                "left": 211, 
                "top": 474
            }, 
            "tool_errors": null, 
            "tool_id": null, 
            "tool_state": "{\"name\": \"R2 fastqs\"}", 
            "tool_version": null, 
            "type": "data_input", 
            "uuid": "59c1e55a-eda7-4570-be94-d2d3dca0eb25", 
            "workflow_outputs": []
        }, 
        "3": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1", 
            "id": 3, 
            "input_connections": {
                "fastq_input|fastq_input1": {
                    "id": 1, 
                    "output_name": "output"
                }, 
                "fastq_input|fastq_input2": {
                    "id": 2, 
                    "output_name": "output"
                }, 
                "reference_source|ref_file": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Map with BWA-MEM", 
            "outputs": [
                {
                    "name": "bam_output", 
                    "type": "bam"
                }
            ], 
            "position": {
                "left": 423.5, 
                "top": 300
            }, 
            "post_job_actions": {
                "RenameDatasetActionbam_output": {
                    "action_arguments": {
                        "newname": "#{fastq_input1 | basename}.bam"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "bam_output"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa_mem/0.7.12.1", 
            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"rg\": \"{\\\"rg_selector\\\": \\\"set_picard\\\", \\\"read_group_sm_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"CN\\\": \\\"\\\", \\\"PU\\\": \\\"\\\", \\\"read_group_lb_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"read_group_id_conditional\\\": {\\\"do_auto_name\\\": \\\"True\\\", \\\"__current_case__\\\": 0}, \\\"__current_case__\\\": 0, \\\"DT\\\": \\\"\\\", \\\"PI\\\": \\\"\\\", \\\"DS\\\": \\\"\\\", \\\"PL\\\": \\\"ILLUMINA\\\"}\", \"fastq_input\": \"{\\\"iset_stats\\\": \\\"\\\", \\\"fastq_input2\\\": null, \\\"fastq_input_selector\\\": \\\"paired\\\", \\\"__current_case__\\\": 0, \\\"fastq_input1\\\": null}\", \"analysis_type\": \"{\\\"analysis_type_selector\\\": \\\"illumina\\\", \\\"__current_case__\\\": 0}\", \"reference_source\": \"{\\\"ref_file\\\": null, \\\"reference_source_selector\\\": \\\"history\\\", \\\"__current_case__\\\": 1, \\\"index_a\\\": \\\"auto\\\"}\"}", 
            "tool_version": "0.7.12.1", 
            "type": "tool", 
            "uuid": "104fb0fa-de5b-4202-a8c3-2e8f0fa1321d", 
            "workflow_outputs": []
        }, 
        "4": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0", 
            "id": 4, 
            "input_connections": {
                "input_bam": {
                    "id": 3, 
                    "output_name": "bam_output"
                }, 
                "ref_file": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "PHE MPileup", 
            "outputs": [
                {
                    "name": "outvcf", 
                    "type": "vcf"
                }
            ], 
            "position": {
                "left": 634, 
                "top": 138
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutvcf": {
                    "action_arguments": {
                        "newname": "#{input_bam | basename}.vcf"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "outvcf"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phe_samtools_mpileup/phe_samtools_mpileup/1.0", 
            "tool_state": "{\"ref_file\": \"null\", \"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input_bam\": \"null\"}", 
            "tool_version": "1.0", 
            "type": "tool", 
            "uuid": "c44a1cad-8e62-4506-84bb-1c4a15f049ca", 
            "workflow_outputs": []
        }, 
        "5": {
            "annotation": "", 
            "content_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", 
            "id": 5, 
            "input_connections": {
                "input": {
                    "id": 4, 
                    "output_name": "outvcf"
                }, 
                "ref_fa": {
                    "id": 0, 
                    "output_name": "output"
                }
            }, 
            "inputs": [], 
            "label": null, 
            "name": "Filter VCF", 
            "outputs": [
                {
                    "name": "output", 
                    "type": "vcf"
                }
            ], 
            "position": {
                "left": 747, 
                "top": 326
            }, 
            "post_job_actions": {
                "RenameDatasetActionoutput": {
                    "action_arguments": {
                        "newname": "#{input | basename}.filtered.vcf"
                    }, 
                    "action_type": "RenameDatasetAction", 
                    "output_name": "output"
                }
            }, 
            "tool_errors": null, 
            "tool_id": "toolshed.g2.bx.psu.edu/repos/ulfschaefer/phephenix/filter_vcf/1.0", 
            "tool_state": "{\"__page__\": 0, \"onlygood\": \"\\\"true\\\"\", \"__rerun_remap_job_id__\": null, \"ref_fa\": \"null\", \"input\": \"null\", \"snp_filter\": \"[{\\\"__index__\\\": 0, \\\"snp_filter_type\\\": {\\\"dp4_ratio\\\": \\\"0.9\\\", \\\"__current_case__\\\": 1, \\\"snp_filter_type_selector\\\": \\\"dp4_ratio_option\\\"}}, {\\\"__index__\\\": 1, \\\"snp_filter_type\\\": {\\\"min_depth\\\": \\\"25\\\", \\\"__current_case__\\\": 4, \\\"snp_filter_type_selector\\\": \\\"min_depth_option\\\"}}, {\\\"__index__\\\": 2, \\\"snp_filter_type\\\": {\\\"mq_score\\\": \\\"30\\\", \\\"__current_case__\\\": 3, \\\"snp_filter_type_selector\\\": \\\"mq_score_option\\\"}}, {\\\"__index__\\\": 3, \\\"snp_filter_type\\\": {\\\"qual_score\\\": \\\"30\\\", \\\"__current_case__\\\": 7, \\\"snp_filter_type_selector\\\": \\\"qual_score_option\\\"}}]\"}", 
            "tool_version": "1.0", 
            "type": "tool", 
            "uuid": "51251f05-75d4-4d89-b757-2248b934d630", 
            "workflow_outputs": []
        }
    }, 
    "uuid": "878b2c0c-3b8a-4800-85fe-2c4f6d47adcf"
}