Ensure pseudoaligner is set if pseudoalignment is not skipped

nf-core · Nov 20, 2023 · 7533e9f · 7533e9f
1 parent 1562e01
commit 7533e9f
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Showing 2 changed files with 8 additions and 2 deletions.
diff --git 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
@@ -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 =