check conda channels as it's done in rnaseq

nf-core · Dec 16, 2022 · 0cb35e6 · 0cb35e6
1 parent 32bf4aa
commit 0cb35e6
Showing 1 changed file with 5 additions and 0 deletions.
diff --git a/nf_core/pipeline-template/lib/WorkflowMain.groovy b/nf_core/pipeline-template/lib/WorkflowMain.groovy
@@ -75,6 +75,11 @@ class WorkflowMain {
         // Check that a -profile or Nextflow config has been provided to run the pipeline
         NfcoreTemplate.checkConfigProvided(workflow, log)
 
+        // Check that conda channels are set-up correctly
+        if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+            Utils.checkCondaChannels(log)
+        }
+
         // Check AWS batch settings
         NfcoreTemplate.awsBatch(workflow, params)