Merge branch 'dev' into samplsheet-for-taxprofiler

.github/workflows/awsfulltest.yml

@@ -19,9 +19,10 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - uses: octokit/[email protected]
+        if: github.event_name != 'workflow_dispatch'
         id: check_approvals
         with:
-          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews
+          route: GET /repos/${{ github.repository }}/pulls/${{ github.event.pull_request.number }}/reviews?per_page=100
         env:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
       - id: test_variables

.nf-core.yml

@@ -18,5 +18,5 @@ template:
   org: nf-core
   outdir: .
   skip_features: null
-  version: 3.1.1dev
+  version: 3.2.0
 update: null

CHANGELOG.md

@@ -3,7 +3,7 @@
 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).
 
-## 3.2.0 [2024-10-25]
+## 3.2.0 [2024-10-27]
 
 ### `Added`
 

conf/modules.config

@@ -263,13 +263,13 @@ process {
     }
 
     withName: METASPADES {
-        ext.args = params.spades_options ?: '--meta'
+        ext.args   = params.spades_options ? params.spades_options + ' --meta' : '--meta'
         ext.prefix = { "SPAdes-${meta.id}" }
         publishDir = [path: { "${params.outdir}/Assembly/SPAdes" }, mode: params.publish_dir_mode, pattern: "*.{fasta.gz,gfa.gz,fa.gz,log}"]
     }
 
     withName: METASPADESHYBRID {
-        ext.args = params.spades_options ?: '--meta'
+        ext.args   = params.spades_options ? params.spades_options + ' --meta' : '--meta'
         ext.prefix = { "SPAdesHybrid-${meta.id}" }
         publishDir = [path: { "${params.outdir}/Assembly/SPAdesHybrid" }, mode: params.publish_dir_mode, pattern: "*.{fasta.gz,gfa.gz,fa.gz,log}"]
     }

conf/test_full.config

@@ -26,8 +26,8 @@ params {
     skip_gtdbtk                = true
 
     // TODO TEMPORARY: deactivate SPAdes due to incompatibility of container with fusion file system
-    skip_spades                = false
-    skip_spadeshybrid          = false
+    skip_spades                = true
+    skip_spadeshybrid          = true
 
     // reproducibility options for assembly
     spades_fix_cpus            = 10