From 7533e9f48da38f303bb7f65b4d74cd182bf918b0 Mon Sep 17 00:00:00 2001
From: Jonathan Manning <jonathan.manning@seqera.io>
Date: Mon, 20 Nov 2023 14:43:01 +0000
Subject: [PATCH] Ensure pseudoaligner is set if pseudoalignment is not skipped

---
 nextflow.config     | 2 +-
 workflows/rnaseq.nf | 8 +++++++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/nextflow.config b/nextflow.config
index d42914210..6a5788e2f 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -58,7 +58,7 @@ params {
 
     // Alignment
     aligner                    = 'star_salmon'
-    pseudo_aligner             = null
+    pseudo_aligner             = 'salmon'
     seq_center                 = null
     bam_csi_index              = false
     star_ignore_sjdbgtf        = false
diff --git a/workflows/rnaseq.nf b/workflows/rnaseq.nf
index 403194ac2..4547162a9 100755
--- a/workflows/rnaseq.nf
+++ b/workflows/rnaseq.nf
@@ -37,7 +37,13 @@ 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 && params.pseudo_aligner) { prepareToolIndices << params.pseudo_aligner }
+if (!params.skip_pseudo_alignment) {
+    if(params.pseudo_aligner) { 
+        prepareToolIndices << params.pseudo_aligner 
+    } else {
+        exit 1, "--skip_pseudo_alignment not set, but --pseudo_aligner not set"
+    }
+}
 
 // Determine whether to filter the GTF or not
 def filterGtf =