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No req input.csv #454

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merged 2 commits into from
Nov 17, 2021
Merged

No req input.csv #454

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bfb1d70
Update nextflow_schema.json
nickhsmith Nov 17, 2021
7898b0f
Update WorkflowMain.groovy
nickhsmith Nov 17, 2021
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6 changes: 0 additions & 6 deletions lib/WorkflowMain.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -71,12 +71,6 @@ class WorkflowMain {

// Check the hostnames against configured profiles
NfcoreTemplate.hostName(workflow, params, log)

// Check input has been provided
if (!params.input) {
log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'"
System.exit(1)
}
}

//
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23 changes: 11 additions & 12 deletions nextflow_schema.json
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Expand Up @@ -11,20 +11,9 @@
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": [
"input",
"step"
],
"properties": {
"input": {
"type": "string",
"format": "file-path",
"mimetype": "text/csv",
"pattern": "\\.csv$",
"schema": "assets/schema_input.json",
"description": "Path to comma-separated file containing information about the samples in the experiment.",
"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with a header row. See [usage docs](https://nf-co.re/sarek/usage#input).",
"fa_icon": "fas fa-file-csv"
},
"step": {
"type": "string",
"default": "mapping",
Expand All @@ -40,6 +29,16 @@
"controlfreec"
]
},
"input": {
"type": "string",
"format": "file-path",
"mimetype": "text/csv",
"pattern": "\\.csv$",
"schema": "assets/schema_input.json",
"description": "Path to comma-separated file containing information about the samples in the experiment.",
"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with a header row. See [usage docs](https://nf-co.re/sarek/usage#input).",
"fa_icon": "fas fa-file-csv"
},
"outdir": {
"type": "string",
"description": "Path to the output directory where the results will be saved.",
Expand Down Expand Up @@ -796,4 +795,4 @@
"$ref": "#/definitions/generic_options"
}
]
}
}