Merge pull request #1039 from drpatelh/updates

Bump pipeline version to 3.12.0

Author: drpatelh

CHANGELOG.md

@@ -3,7 +3,20 @@
 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).
 
-## [Unpublished Version / DEV]
+## [[3.12.0](https://github.com/nf-core/rnaseq/releases/tag/3.12.0)] - 2023-06-02
+
+### Credits
+
+Special thanks to the following for their contributions to the release:
+
+- [Adam Talbot](https://github.com/adamrtalbot)
+- [Esha Joshi](https://github.com/ejseqera)
+- [Ghepardo](https://github.com/Ghepardo)
+- [Matthias Zepper](https://github.com/MatthiasZepper)
+- [Maxime Garcia](https://github.com/maxulysse)
+- [Rob Syme](https://github.com/robsyme)
+
+Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form.
 
 ### Enhancements & fixes
 

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 {

nextflow.config

@@ -302,7 +302,7 @@ manifest {
     description     = """RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control."""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=22.10.1'
-    version         = '3.12.0dev'
+    version         = '3.12.0'
     doi             = 'https://doi.org/10.5281/zenodo.1400710'
 }
 

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() } : []