Be more explicit with --skip_pseudo_aligner logic

nf-core · Jun 1, 2023 · 993fff6 · 993fff6
1 parent 84890da
commit 993fff6
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Showing 2 changed files with 2 additions and 2 deletions.
diff --git a/lib/WorkflowRnaseq.groovy b/lib/WorkflowRnaseq.groovy
@@ -68,7 +68,7 @@ class WorkflowRnaseq {
             skipAlignmentWarn(log)
         }
 
-        if (!params.skip_pseudo_alignment) {
+        if (!params.skip_pseudo_alignment && params.pseudo_aligner) {
             if (!valid_params['pseudoaligners'].contains(params.pseudo_aligner)) {
                 Nextflow.error("Invalid option: '${params.pseudo_aligner}'. Valid options for '--pseudo_aligner': ${valid_params['pseudoaligners'].join(', ')}.")
             } else {

diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf
@@ -45,7 +45,7 @@ if (!params.skip_bbsplit && !params.bbsplit_index && params.bbsplit_fasta_list)
 def prepareToolIndices  = []
 if (!params.skip_bbsplit) { prepareToolIndices << 'bbsplit' }
 if (!params.skip_alignment) { prepareToolIndices << params.aligner }
-if (!params.skip_pseudo_alignment) { prepareToolIndices << params.pseudo_aligner }
+if (!params.skip_pseudo_alignment && params.pseudo_aligner) { prepareToolIndices << params.pseudo_aligner }
 
 // Get RSeqC modules to run
 def rseqc_modules = params.rseqc_modules ? params.rseqc_modules.split(',').collect{ it.trim().toLowerCase() } : []