nf-core · mirpedrol · Feb 23, 2023 · Feb 23, 2023 · Feb 23, 2023 · May 16, 2023
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,8 @@
 - Move registry definitions out of profile scope ([#2286])(https://github.com/nf-core/tools/pull/2286)
 - Remove `aws_tower` profile ([#2287])(https://github.com/nf-core/tools/pull/2287)
 - Fixed the Slack report to include the pipeline name ([#2291](https://github.com/nf-core/tools/pull/2291))
+- Remove shcema validation from `lib` folder and use Nextflow nf-validation plugin instead ([#1771](https://github.com/nf-core/tools/pull/1771/))
- Remove shcema validation from `lib` folder and use Nextflow nf-validation plugin instead ([#1771](https://github.com/nf-core/tools/pull/1771/))
+- Remove schema validation from `lib` folder and use Nextflow nf-validation plugin instead ([#1771](https://github.com/nf-core/tools/pull/1771/))
- Remove shcema validation from `lib` folder and use Nextflow nf-validation plugin instead ([#1771](https://github.com/nf-core/tools/pull/1771/))
+- Remove schema validation from `lib` folder and use Nextflow nf-validation plugin instead ([#1771](https://github.com/nf-core/tools/pull/1771/))
+- Generate input channel from input file using Nextflow nf-validation plugin ([#1771](https://github.com/nf-core/tools/pull/1771/))
 
 ### Linting
 

diff --git a/nf_core/lint/files_exist.py b/nf_core/lint/files_exist.py
@@ -52,7 +52,6 @@ def files_exist(self):
         docs/README.md
         docs/usage.md
         lib/nfcore_external_java_deps.jar
-        lib/NfcoreSchema.groovy
         lib/NfcoreTemplate.groovy
         lib/Utils.groovy
         lib/WorkflowMain.groovy
@@ -161,7 +160,6 @@ def files_exist(self):
         [os.path.join("docs", "README.md")],
         [os.path.join("docs", "usage.md")],
         [os.path.join("lib", "nfcore_external_java_deps.jar")],
-        [os.path.join("lib", "NfcoreSchema.groovy")],
         [os.path.join("lib", "NfcoreTemplate.groovy")],
         [os.path.join("lib", "Utils.groovy")],
         [os.path.join("lib", "WorkflowMain.groovy")],

diff --git a/nf_core/lint/files_unchanged.py b/nf_core/lint/files_unchanged.py
@@ -40,7 +40,6 @@ def files_unchanged(self):
         docs/images/nf-core-PIPELINE_logo_dark.png
         docs/README.md'
         lib/nfcore_external_java_deps.jar
-        lib/NfcoreSchema.groovy
         lib/NfcoreTemplate.groovy
         ['LICENSE', 'LICENSE.md', 'LICENCE', 'LICENCE.md'], # NB: British / American spelling
 
@@ -105,7 +104,6 @@ def files_unchanged(self):
         [os.path.join("docs", "images", f"nf-core-{short_name}_logo_dark.png")],
         [os.path.join("docs", "README.md")],
         [os.path.join("lib", "nfcore_external_java_deps.jar")],
-        [os.path.join("lib", "NfcoreSchema.groovy")],
         [os.path.join("lib", "NfcoreTemplate.groovy")],
     ]
     files_partial = [

diff --git a/nf_core/lint/nextflow_config.py b/nf_core/lint/nextflow_config.py
@@ -62,7 +62,7 @@ def nextflow_config(self):
         * Should always be set to default value:
         ``https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}``
 
-    * ``params.show_hidden_params``
+    * ``params.validationShowHiddenParams``
 
         * Determines whether boilerplate params are showed by schema. Set to ``false`` by default
 
@@ -130,8 +130,6 @@ def nextflow_config(self):
         ["process.time"],
         ["params.outdir"],
         ["params.input"],
-        ["params.show_hidden_params"],
-        ["params.schema_ignore_params"],
     ]
     # Throw a warning if these are missing
     config_warn = [

diff --git a/nf_core/pipeline-template/assets/schema_input.json b/nf_core/pipeline-template/assets/schema_input.json
@@ -10,7 +10,8 @@
             "sample": {
                 "type": "string",
                 "pattern": "^\\S+$",
-                "errorMessage": "Sample name must be provided and cannot contain spaces"
+                "errorMessage": "Sample name must be provided and cannot contain spaces",
+                "meta": ["id"]
             },
             "fastq_1": {
                 "type": "string",

diff --git a/nf_core/pipeline-template/bin/check_samplesheet.py b/nf_core/pipeline-template/bin/check_samplesheet.py
diff --git a/nf_core/pipeline-template/conf/modules.config b/nf_core/pipeline-template/conf/modules.config
@@ -18,14 +18,6 @@ process {
         saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
     ]
 
-    withName: SAMPLESHEET_CHECK {
-        publishDir = [
-            path: { "${params.outdir}/pipeline_info" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
     withName: FASTQC {
         ext.args = '--quiet'
     }