diff --git a/CHANGELOG.md b/CHANGELOG.md index 8b086ff..338faa3 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -11,8 +11,7 @@ Initial release of nf-core/nanostring, created with the [nf-core](https://nf-co. ### `Fixed` -### `Changed` - +- [#133](https://github.com/nf-core/nanostring/pull/133/) - Improvements to JSON schema and minor linting changes - [#136](https://github.com/nf-core/nanostring/pull/136) - Replaced `NORMALIZE` and `QUALITY_CONTROL` for its modules. ### `Dependencies` diff --git a/nextflow_schema.json b/nextflow_schema.json index 9bd4089..f939a7f 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -28,18 +28,6 @@ "format": "directory-path", "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", "fa_icon": "fas fa-folder-open" - }, - "email": { - "type": "string", - "description": "Email address for completion summary.", - "fa_icon": "fas fa-envelope", - "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.", - "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$" - }, - "multiqc_title": { - "type": "string", - "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.", - "fa_icon": "fas fa-file-signature" } } }, @@ -71,6 +59,7 @@ "normalization_method": { "type": "string", "default": "GEO", + "enum": ["GEO", "GLM"], "fa_icon": "fas fa-compress-arrows-alt", "description": "The method to use for normalization of nCounter data.", "help_text": "Available options are `GEO` (default) or `GLM`." @@ -91,7 +80,7 @@ "description": "This selects the algorithm for computing the respective gene score. Default is 'plage.dir'." }, "gene_score_yaml": { - "type": "string", + "format": "file-path", "fa_icon": "fas fa-align-justify", "help_text": "The YAML format is as such:\n\n```\nscore_name: \n - GENE1\n - GENE2\n - GENE3\n```", "description": "This sets the YAML to be used for computing the gene scores. Needs both a name for each set of genes and respective genes to be selected." @@ -209,6 +198,13 @@ "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], "hidden": true }, + "email": { + "type": "string", + "description": "Email address for completion summary.", + "fa_icon": "fas fa-envelope", + "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.", + "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$" + }, "email_on_fail": { "type": "string", "description": "Email address for completion summary, only when pipeline fails.", @@ -244,6 +240,11 @@ "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.", "hidden": true }, + "multiqc_title": { + "type": "string", + "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.", + "fa_icon": "fas fa-file-signature" + }, "multiqc_config": { "type": "string", "format": "file-path",