{
    "a_galaxy_workflow": "true",
    "annotation": "From the R1 and R2 fastq files of a single samples, make a scRNAseq counts matrix, and perform basic QC with scanpy. Then, do further processing by making a UMAP and clustering. Produces a processed AnnData \n",
    "format-version": "0.1",
    "name": "scRNAseq Single Sample Processing STARSolo",
    "report": {
        "markdown": "\n# Single-cell RNAseq Processing Workflow report\n\nPlease refer to the two sub-workflow reports - QC and basic processing.\n\n## Workflow\n```galaxy\nworkflow_display()\n```\n\n\n"
    },
    "steps": {
        "0": {
            "annotation": "Typically the Forward reads are labelled _R1, barcodes. R2 is Reverse, mRNA sequences. List should contain seq for one biological sample only.",
            "content_id": null,
            "errors": null,
            "id": 0,
            "input_connections": {},
            "inputs": [
                {
                    "description": "Typically the Forward reads are labelled _R1, barcodes. R2 is Reverse, mRNA sequences. List should contain seq for one biological sample only.",
                    "name": "Paired Fastqs for one sample"
                }
            ],
            "label": "Paired Fastqs for one sample",
            "name": "Input dataset collection",
            "outputs": [],
            "position": {
                "left": 24.4921875,
                "top": 0
            },
            "tool_id": null,
            "tool_state": "{\"optional\": false, \"tag\": \"\", \"collection_type\": \"list:paired\"}",
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            "type": "data_collection_input",
            "uuid": "ef76d6f2-fb39-4a6c-a7bf-e344c7346c62",
            "workflow_outputs": []
        },
        "1": {
            "annotation": "Fasta sequence of reference genome used. ",
            "content_id": null,
            "errors": null,
            "id": 1,
            "input_connections": {},
            "inputs": [
                {
                    "description": "Fasta sequence of reference genome used. ",
                    "name": "Reference Genome"
                }
            ],
            "label": "Reference Genome",
            "name": "Input dataset",
            "outputs": [],
            "position": {
                "left": 0.0,
                "top": 139.9765625
            },
            "tool_id": null,
            "tool_state": "{\"optional\": false, \"tag\": \"\"}",
            "tool_version": null,
            "type": "data_input",
            "uuid": "4f20308e-02dc-45f0-9f0a-35b5a62dc9e2",
            "workflow_outputs": []
        },
        "2": {
            "annotation": "Gtf of Gff3 file with gene coordinates and annotation. Ensembl downloads are suitable.",
            "content_id": null,
            "errors": null,
            "id": 2,
            "input_connections": {},
            "inputs": [
                {
                    "description": "Gtf of Gff3 file with gene coordinates and annotation. Ensembl downloads are suitable.",
                    "name": "Reference Annotation"
                }
            ],
            "label": "Reference Annotation",
            "name": "Input dataset",
            "outputs": [],
            "position": {
                "left": 4.9765625,
                "top": 246.9921875
            },
            "tool_id": null,
            "tool_state": "{\"optional\": false, \"tag\": \"\"}",
            "tool_version": null,
            "type": "data_input",
            "uuid": "79345038-2d73-4cd8-957b-8bf968dfd18b",
            "workflow_outputs": []
        },
        "3": {
            "annotation": "Short, unique and meaningful name of this sample. ",
            "content_id": null,
            "errors": null,
            "id": 3,
            "input_connections": {},
            "inputs": [
                {
                    "description": "Short, unique and meaningful name of this sample. ",
                    "name": "Sample ID"
                }
            ],
            "label": "Sample ID",
            "name": "Input parameter",
            "outputs": [],
            "position": {
                "left": 34.96875,
                "top": 455.9921875
            },
            "tool_id": null,
            "tool_state": "{\"parameter_type\": \"text\", \"optional\": false}",
            "tool_version": null,
            "type": "parameter_input",
            "uuid": "27d0ddc6-16ba-40a4-9dab-b66bd48332da",
            "workflow_outputs": [
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                    "label": null,
                    "output_name": "output",
                    "uuid": "72ded31f-cd26-43cc-bc94-719213b58ddd"
                }
            ]
        },
        "4": {
            "annotation": "List of possible cell barcodes. Depends on the kit used.",
            "content_id": null,
            "errors": null,
            "id": 4,
            "input_connections": {},
            "inputs": [
                {
                    "description": "List of possible cell barcodes. Depends on the kit used.",
                    "name": "Barcode Whitelist"
                }
            ],
            "label": "Barcode Whitelist",
            "name": "Input dataset",
            "outputs": [],
            "position": {
                "left": 33.03125,
                "top": 555.921875
            },
            "tool_id": null,
            "tool_state": "{\"optional\": false, \"tag\": \"\"}",
            "tool_version": null,
            "type": "data_input",
            "uuid": "6d2b114e-3a91-4a0e-816f-ec1e6b05e954",
            "workflow_outputs": []
        },
        "5": {
            "annotation": "How many cells are expected to be sequenced in this sample?",
            "content_id": null,
            "errors": null,
            "id": 5,
            "input_connections": {},
            "inputs": [
                {
                    "description": "How many cells are expected to be sequenced in this sample?",
                    "name": "Expected cells"
                }
            ],
            "label": "Expected cells",
            "name": "Input parameter",
            "outputs": [],
            "position": {
                "left": 31.9609375,
                "top": 660.953125
            },
            "tool_id": null,
            "tool_state": "{\"default\": 2000, \"parameter_type\": \"integer\", \"optional\": true}",
            "tool_version": null,
            "type": "parameter_input",
            "uuid": "19e5067a-550d-483b-a19a-0d8dfa8cd6c3",
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                    "output_name": "output",
                    "uuid": "0dbb08b3-8379-4186-9bf3-6bc6f4798292"
                }
            ]
        },
        "6": {
            "annotation": "Prefix on mitochondrial gene names. Default MT- typical for human, mt- for mouse. If mitochondrial genes are not prefixed, Mito flagging, plotting and filtering steps will need to be removed.",
            "content_id": null,
            "errors": null,
            "id": 6,
            "input_connections": {},
            "inputs": [
                {
                    "description": "Prefix on mitochondrial gene names. Default MT- typical for human, mt- for mouse. If mitochondrial genes are not prefixed, Mito flagging, plotting and filtering steps will need to be removed.",
                    "name": "Mitochondrial Prefix"
                }
            ],
            "label": "Mitochondrial Prefix",
            "name": "Input parameter",
            "outputs": [],
            "position": {
                "left": 783.96875,
                "top": 795.4296875
            },
            "tool_id": null,
            "tool_state": "{\"default\": \"MT-\", \"suggestions\": [\"MT-\", \"mt-\", \"Mt-\"], \"parameter_type\": \"text\", \"optional\": true}",
            "tool_version": null,
            "type": "parameter_input",
            "uuid": "5e15c021-a0a9-49f1-8f15-1b85f2c258a2",
            "workflow_outputs": [
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                    "label": null,
                    "output_name": "output",
                    "uuid": "d65ad8ab-b977-4df8-94e2-37343742366a"
                }
            ]
        },
        "7": {
            "annotation": "Cells with fewer than this number of total counts will be removed.",
            "content_id": null,
            "errors": null,
            "id": 7,
            "input_connections": {},
            "inputs": [
                {
                    "description": "Cells with fewer than this number of total counts will be removed.",
                    "name": "MinCountPerCell"
                }
            ],
            "label": "MinCountPerCell",
            "name": "Input parameter",
            "outputs": [],
            "position": {
                "left": 810.9609375,
                "top": 907.2265625
            },
            "tool_id": null,
            "tool_state": "{\"default\": 1000.0, \"parameter_type\": \"float\", \"optional\": true}",
            "tool_version": null,
            "type": "parameter_input",
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                    "output_name": "output",
                    "uuid": "3292f4c5-42b5-4def-bd1c-9e2961bf413f"
                }
            ]
        },
        "8": {
            "annotation": "Cells with fewer than this many distinct genes observed will be removed.",
            "content_id": null,
            "errors": null,
            "id": 8,
            "input_connections": {},
            "inputs": [
                {
                    "description": "Cells with fewer than this many distinct genes observed will be removed.",
                    "name": "MinGenesPerCell"
                }
            ],
            "label": "MinGenesPerCell",
            "name": "Input parameter",
            "outputs": [],
            "position": {
                "left": 826.578125,
                "top": 1013.625
            },
            "tool_id": null,
            "tool_state": "{\"default\": 500.0, \"parameter_type\": \"float\", \"optional\": true}",
            "tool_version": null,
            "type": "parameter_input",
            "uuid": "43dd6429-bc23-491d-bf65-6c3ba0ba067c",
            "workflow_outputs": [
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                    "output_name": "output",
                    "uuid": "adf01f52-4ac3-47e5-9d4a-b237ad6127f6"
                }
            ]
        },
        "9": {
            "annotation": "Cells with more than this percentage of counts coming from mitochondrial genes will be removed. ",
            "content_id": null,
            "errors": null,
            "id": 9,
            "input_connections": {},
            "inputs": [
                {
                    "description": "Cells with more than this percentage of counts coming from mitochondrial genes will be removed. ",
                    "name": "MaxMTpc"
                }
            ],
            "label": "MaxMTpc",
            "name": "Input parameter",
            "outputs": [],
            "position": {
                "left": 885.578125,
                "top": 1077.640625
            },
            "tool_id": null,
            "tool_state": "{\"default\": 30.0, \"parameter_type\": \"float\", \"optional\": true}",
            "tool_version": null,
            "type": "parameter_input",
            "uuid": "4484fca3-1a56-46cc-8f1d-fd2df8fb6f51",
            "workflow_outputs": [
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                    "output_name": "output",
                    "uuid": "74430648-58a6-4643-809e-b0d569b2c6fd"
                }
            ]
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            "annotation": "",
            "id": 10,
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                    "input_subworkflow_step_id": 4,
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                },
                "Paired Fastqs for one sample": {
                    "id": 0,
                    "input_subworkflow_step_id": 0,
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                "Reference Genome fasta": {
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                    "input_subworkflow_step_id": 5,
                    "output_name": "output"
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            },
            "inputs": [],
            "label": null,
            "name": "scRNAseq: Count and Load with starSOLO",
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            },
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                "annotation": "",
                "format-version": "0.1",
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                        "tool_id": null,
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                                "name": "Reference Genome fasta"
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                        "label": "Reference Genome fasta",
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                            "top": 0
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                        "id": 2,
                        "input_connections": {},
                        "inputs": [
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                                "name": "Reference annotation"
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                        "id": 3,
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                                "name": "Barcode Whitelist file"
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                        "inputs": [
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                                "name": "Expected Cells"
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                        ],
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