added aligner check in main.nf

nf-core · Oct 29, 2024 · b6f0f12 · b6f0f12
1 parent 5cbc66a
commit b6f0f12
Showing 1 changed file with 2 additions and 6 deletions.
diff --git a/workflows/sarek/main.nf b/workflows/sarek/main.nf
@@ -241,6 +241,8 @@ workflow SAREK {
             reads_for_fastp = input_fastq
         }
 
+        params.aligner = 'parabricks' ? params.split_fastq = 0 : params.split_fastq
+
         // Trimming and/or splitting
         if (params.trim_fastq || params.split_fastq > 0) {
 
@@ -257,12 +259,6 @@ workflow SAREK {
             reports = reports.mix(FASTP.out.json.collect{ meta, json -> json })
             reports = reports.mix(FASTP.out.html.collect{ meta, html -> html })
 
-            if (params.aligner = 'parabricks') {
-
-                params.split_fastq = 0
-
-            }
-
             if (params.split_fastq) {
                 reads_for_alignment = FASTP.out.reads.map{ meta, reads ->
                     read_files = reads.sort(false) { a,b -> a.getName().tokenize('.')[0] <=> b.getName().tokenize('.')[0] }.collate(2)