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Merge pull request #80 from adamrtalbot/patch-1
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Update fromSamplesheet.md wording slightly.
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nvnieuwk committed Jul 26, 2023
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10 changes: 4 additions & 6 deletions docs/samplesheets/fromSamplesheet.md
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Expand Up @@ -7,11 +7,9 @@ description: Channel factory to create a channel from a sample sheet.

## `fromSamplesheet`

This function validates and converts a samplesheet to a ready-to-use Nextflow channel.
This is done using information encoded within a sample sheet schema (see the [docs](../nextflow_schema/sample_sheet_schema_specification.md)).
This function validates and converts a samplesheet to a ready-to-use Nextflow channel. This is done using information encoded within a sample sheet schema (see the [docs](../nextflow_schema/sample_sheet_schema_specification.md)).

The function has one mandatory argument: a string specifying the name of the parameter used to provide a samplesheet.
This parameter be described in the Nextflow parameter schema using as a file, with a `schema` field:
The function has one mandatory argument: the name of the parameter which specifies the input samplesheet. The parameter specified must have the format `file-path` and include additional field `schema`:

```json hl_lines="4"
{
Expand All @@ -21,9 +19,9 @@ This parameter be described in the Nextflow parameter schema using as a file, wi
}
```

The given sample sheet schema specified in the `schema` key is then loaded and used for validation and sample sheet generation.
The path specified in the `schema` key determines the JSON used for validation of the samplesheet.

Some additional function optional arguments can be used:
When using the `.fromSamplesheet` channel factory, some additional optional arguments can be used:

- `schema_filename`: File name for the pipeline parameters schema. (Default: `nextflow_schema.json`)
- `skip_duplicate_check`: Skip the checking for duplicates. Can also be skipped with the `--validationSkipDuplicateCheck` parameter. (Default: `false`)
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