From 6da07872a8832902f78af7315d9e0411860bb465 Mon Sep 17 00:00:00 2001
From: Gregor Sturm <gregor.sturm@boehringer-ingelheim.com>
Date: Mon, 12 Aug 2024 13:13:53 +0200
Subject: [PATCH 1/2] Re-enable schema linting

---
 .nf-core.yml    | 3 ---
 nextflow.config | 5 -----
 2 files changed, 8 deletions(-)

diff --git a/.nf-core.yml b/.nf-core.yml
index 73506c0f..7c377491 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -6,6 +6,3 @@ lint:
     - .github/ISSUE_TEMPLATE/bug_report.yml
   files_exist:
     - lib/Utils.groovy
-  # TODO This is because of an issue with the monochromeLogs parameter
-  # See nextflow.config for details
-  schema_params: False
diff --git a/nextflow.config b/nextflow.config
index 868f5e3a..07ae3e2b 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -114,11 +114,6 @@ params {
     validationShowHiddenParams       = false
     validate_params                  = true
 
-    // TODO temporary workaround a warning
-    // not used anywhere and should not be necessary anymore after a nf-validation plugin update
-    // TODO when removing this, also remove the ignored lint check from .nf-core.yml
-    monochromeLogs = null
-
 }
 
 // Load base.config by default for all pipelines

From c918195b043ecee94525106ffbb563664dc2e225 Mon Sep 17 00:00:00 2001
From: Gregor Sturm <gregor.sturm@boehringer-ingelheim.com>
Date: Mon, 12 Aug 2024 16:40:08 +0200
Subject: [PATCH 2/2] Add missing options to nextflow.config

---
 CHANGELOG.md    | 1 +
 nextflow.config | 2 ++
 2 files changed, 3 insertions(+)

diff --git a/CHANGELOG.md b/CHANGELOG.md
index 56d020cf..9217c819 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+- Re-enable linting check for nextflow schema ([#354](https://github.com/nf-core/scrnaseq/pull/354))
 - Add support for 10XV4 chemistry ([#348](https://github.com/nf-core/scrnaseq/pull/348))
 - Fix issues with predefined STAR index ([#350](https://github.com/nf-core/scrnaseq/pull/350))
 - Update modules ([#351](https://github.com/nf-core/scrnaseq/pull/351))
diff --git a/nextflow.config b/nextflow.config
index 07ae3e2b..34dc69fd 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -19,6 +19,8 @@ params {
     genome            = null
     transcript_fasta  = null
     txp2gene          = null
+    fasta             = null
+    gtf               = null
 
     // salmon alevin parameters (simpleaf)
     simpleaf_rlen     = 91