From 5bd456e5e8cdc9cf8a34ce9bc5fc1f949714e0fe Mon Sep 17 00:00:00 2001
From: Rike <friederike.hanssen@qbic.uni-tuebingen.de>
Date: Mon, 9 May 2022 16:06:22 +0200
Subject: [PATCH] rename file_type to output extension

---
 modules/samtools/convert/main.nf | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/samtools/convert/main.nf b/modules/samtools/convert/main.nf
index b20f2b93..4638d360 100644
--- a/modules/samtools/convert/main.nf
+++ b/modules/samtools/convert/main.nf
@@ -21,8 +21,8 @@ process SAMTOOLS_CONVERT {
 
     script:
     def args = task.ext.args  ?: ''
-    prefix = task.ext.prefix ?: "${meta.id}"
-    def file_type = input.getExtension() == "bam" ? "cram" : "bam"
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def output_extension = input.getExtension() == "bam" ? "cram" : "bam"
 
     """
     samtools view \\
@@ -30,9 +30,9 @@ process SAMTOOLS_CONVERT {
         --reference ${fasta} \\
         $args \\
         $input \\
-        -o ${prefix}.${file_type}
+        -o ${prefix}.${output_extension}
 
-    samtools index -@${task.cpus} ${prefix}.${file_type}
+    samtools index -@${task.cpus} ${prefix}.${output_extension}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":