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Launch parameter validation for --input failing on valid input #847

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ameynert opened this issue Nov 16, 2022 · 1 comment
Closed

Launch parameter validation for --input failing on valid input #847

ameynert opened this issue Nov 16, 2022 · 1 comment
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@ameynert
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Description of the bug

https://nf-co.re/launch for Sarek fails when e.g. "samplesheet.csv" is provided in for --input. This should pass the regular expression .csv$.

Screenshot 2022-11-16 at 10 24 50

Possibly only needs one \ in nextflow_schema.json:

                "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": "A design file with information about the samples in your experiment. Use this parameter to specify the location of the input files. It has to be a comma-separated file with a header row. See [usage docs](https://nf-co.re/sarek/usage#input).\n\nIf no input file is specified, sarek will attempt to locate one in the `{outdir}` directory.",
                    "fa_icon": "fas fa-file-csv"
                },

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@ameynert ameynert added the bug Something isn't working label Nov 16, 2022
@FriederikeHanssen
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Fixed on dev, release incoming, see also: #694

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