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Upgrade schema #9

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65 changes: 41 additions & 24 deletions flow/schema/main.json
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Original file line number Diff line number Diff line change
@@ -1,42 +1,59 @@
{
"inputs": {
"input_data": {
"inputs": [
{
"name": "Input Data",
"description": "Required input data",
"advanced": false,
"properties": {
"modes": ["Flow Samples", "Provide File"],
"params": {
"samplesheet": {
"name": "Samples",
"type": "sample",
"pattern": "csv|xlsx",
"required": true,
"description": "A list of sample IDs with their condition indicator. The sample IDs here must match those used in the corresponding counts file. You can provide additional columns if you wish.",
"required": true,
"modes": ["Flow Samples"],
"type": "csv",
"takes_samples": true,
"allow_custom_columns": true,
"csv": {
"sample_id": {
"property": "name",
"user_override": true
"columns": [
{
"name": "sample_id",
"type": "string",
"from_sample": "name",
"required": true,
"render": true
},
"condition": {
"property": "",
"user_override": true
{
"name": "condition",
"type": "string",
"required": true,
"render": true
}
}
]
},
"samplesheet_": {
"key": "samplesheet",
"name": "Samples",
"description": "A list of sample IDs with their condition indicator. The sample IDs here must match those used in the corresponding counts file. You can provide additional columns if you wish.",
"required": true,
"modes": ["Provide File"],
"type": "data",
"pattern": "csv|xlsx"
},
"counts": {
"name": "Counts",
"type": "file",
"type": "data",
"modes": ["Flow Samples", "Provide File"],
"pattern": "csv|tsv",
"required": true,
"description": "A table file with whole number counts."
}
}
},
"parameters": {
{
"name": "Pipeline Options",
"description": "Pipeline run parameters",
"advanced": false,
"properties": {
"params": {
"study_name": {
"name": "Study Name",
"description": "The name of the study.",
Expand Down Expand Up @@ -89,11 +106,11 @@
}
}
},
"advanced_parameters": {
{
"name": "Advanced Pipeline Options",
"description": "Advanced Pipeline run parameters",
"advanced": true,
"properties": {
"params": {
"count_sep": {
"name": "Count separator",
"description": "The text delimiter which separates columns in the input count matrix file.",
Expand All @@ -102,11 +119,11 @@
}
}
},
"deseq_parameters": {
{
"name": "Advanced DESeq2 Options",
"description": "Advanced DESeq2 parameters",
"advanced": true,
"properties": {
"params": {
"dsq_test": {
"name": "Test type",
"description": "DESeq2 test type.",
Expand Down Expand Up @@ -177,11 +194,11 @@
}
}
},
"gsea_parameters": {
{
"name": "Advanced GSEA Options",
"description": "Advanced GSEA parameters",
"advanced": true,
"properties": {
"params": {
"dsq_p_thresh": {
"name": "DESeq2 p-value Threshold",
"description": "p-value cut off for filtering input deseq2 results table.",
Expand Down Expand Up @@ -279,7 +296,7 @@
}
}
}
},
],
"outputs": [
{
"name": "DESeq2 rds data file",
Expand Down