diff --git a/docs/samplesheets/fromSamplesheet.md b/docs/samplesheets/fromSamplesheet.md index acf1e789..3cbcf9e5 100644 --- a/docs/samplesheets/fromSamplesheet.md +++ b/docs/samplesheets/fromSamplesheet.md @@ -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" { @@ -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`)