Merge remote-tracking branch 'origin/dev' into fix-multiqc

.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

CHANGELOG.md

@@ -3,8 +3,9 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased]
+## v2.7.1 - 2024-08-13
 
+- 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))

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/scrnaseq/tree/dev" target="_blank">nf-core/scrnaseq</a>
+  This report has been generated by the <a href="https://github.com/nf-core/scrnaseq/releases/tag/2.7.1" target="_blank">nf-core/scrnaseq</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/scrnaseq/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/scrnaseq/2.7.1/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-scrnaseq-methods-description":
     order: -1000

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
@@ -114,11 +116,6 @@ 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
@@ -303,7 +300,7 @@ manifest {
     description     = """Pipeline for processing 10x Genomics single cell rnaseq data"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '2.8.0dev'
+    version         = '2.7.1'
     doi             = '10.5281/zenodo.3568187'
 }