Be more explicit with --skip_pseudo_aligner logic

Author: drpatelh

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 {

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() } : []