nf-core · ramprasadn · Jul 26, 2023 · Jul 24, 2023 · Jul 24, 2023 · Jul 24, 2023
diff --git a/.nf-core.yml b/.nf-core.yml
@@ -5,4 +5,5 @@ lint:
     - .github/PULL_REQUEST_TEMPLATE.md
     - assets/multiqc_config.yaml
     - .github/workflows/linting.yml
+    - pyproject.toml
 repository_type: pipeline
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,9 +7,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Added`
 
+- Use `nf-validation` plugin for parameter and samplesheet validation [#386](https://github.com/nf-core/raredisease/pull/386)
+
 ### `Changed`
 
-- Tiddit updated to v3.6.1 [#385](https://github.com/nf-core/sarek/pull/385)
+- Tiddit updated to v3.6.1 [#385](https://github.com/nf-core/raredisease/pull/385)
 
 ### `Fixed`
 

diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -9,11 +9,19 @@
         "properties": {
             "sample": {
                 "type": "string",
+                "exists": true,
+                "meta": ["id"],
                 "pattern": "^\\S+$",
                 "errorMessage": "Sample name must be provided and cannot contain spaces"
             },
+            "lane": {
+                "type": "number",
+                "meta": ["lane"]
+            },
             "fastq_1": {
                 "type": "string",
+                "format": "file-path",
+                "exists": true,
                 "pattern": "^\\S+\\.f(ast)?q\\.gz$",
                 "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
             },
@@ -32,16 +40,19 @@
             },
             "sex": {
                 "type": "string",
+                "meta": ["sex"],
                 "pattern": "^\\S+$",
                 "errorMessage": "Sex must be provided and cannot contain spaces"
             },
             "phenotype": {
                 "type": "string",
+                "meta": ["phenotype"],
                 "pattern": "^\\S+$",
                 "errorMessage": "Phenotype must be provided and cannot contain spaces"
             },
             "paternal_id": {
                 "errorMessage": "Paternal ID cannot contain spaces",
+                "meta": ["paternal"],
                 "anyOf": [
                     {
                         "type": "string",
@@ -55,6 +66,7 @@
             },
             "maternal_id": {
                 "errorMessage": "Maternal ID cannot contain spaces",
+                "meta": ["maternal"],
                 "anyOf": [
                     {
                         "type": "string",
@@ -68,6 +80,7 @@
             },
             "case_id": {
                 "type": "string",
+                "meta": ["case_id"],
                 "pattern": "^\\S+$",
                 "errorMessage": "Case name must be provided and cannot contain spaces"
             }

diff --git a/conf/modules/raredisease.config b/conf/modules/raredisease.config
@@ -17,14 +17,6 @@
 
 process {
 
-    withName: '.*CHECK_INPUT:SAMPLESHEET_CHECK' {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
     withName: 'CUSTOM_DUMPSOFTWAREVERSIONS' {
         publishDir = [
             path: { "${params.outdir}/pipeline_info" },

diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf
diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -10,12 +10,13 @@
             "type": "object",
             "fa_icon": "fas fa-terminal",
             "description": "Define where the pipeline should find input data and save output data.",
-            "required": ["input", "outdir"],
+            "required": ["outdir"],
             "properties": {
                 "input": {
                     "type": "string",
                     "format": "file-path",
                     "exists": true,
+                    "schema": "assets/schema_input.json",
                     "mimetype": "text/csv",
                     "pattern": "^\\S+\\.csv$",
                     "description": "Path to comma-separated file containing information about the samples in the experiment.",
@@ -621,18 +622,23 @@
                 "multiqc_config": {
                     "type": "string",
                     "format": "file-path",
+                    "exists": true,
                     "description": "Custom config file to supply to MultiQC.",
                     "fa_icon": "fas fa-cog",
                     "hidden": true
                 },
                 "multiqc_logo": {
                     "type": "string",
+                    "format": "file-path",
+                    "exists": true,
                     "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file",
                     "fa_icon": "fas fa-image",
                     "hidden": true
                 },
                 "multiqc_methods_description": {
                     "type": "string",
+                    "format": "file-path",
+                    "exists": true,
                     "description": "Custom MultiQC yaml file containing HTML including a methods description.",
                     "fa_icon": "fas fa-cog",
                     "hidden": true

diff --git a/pyproject.toml b/pyproject.toml
@@ -1,4 +1,4 @@
-# Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Black.
+# Config file for Python. Mostly used to configure linting of bin/*.py with Black.
 # Should be kept the same as nf-core/tools to avoid fighting with template synchronisation.
 [tool.black]
 line-length = 120

diff --git a/subworkflows/local/check_input.nf b/subworkflows/local/check_input.nf
diff --git a/tower.yml b/tower.yml
@@ -1,8 +1,6 @@
 reports:
   multiqc_report.html:
     display: "MultiQC HTML report"
-  samplesheet.valid.csv:
-    display: "Auto-created samplesheet with collated metadata and FASTQ paths"
   "*.ped":
     display: "Auto-created pedigree file"
     mimeType: "text"