From a7c125b61a5e6a3d49bb519e5665c0cf99f69e05 Mon Sep 17 00:00:00 2001
From: Tyler Chafin <tc25@sanger.ac.uk>
Date: Thu, 11 Jul 2024 16:51:49 +0100
Subject: [PATCH] Update modules/local/samtools_replaceheader.nf

Co-authored-by: Matthieu Muffato <cortexspam-github@yahoo.fr>
---
 modules/local/samtools_replaceheader.nf | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/modules/local/samtools_replaceheader.nf b/modules/local/samtools_replaceheader.nf
index 06e45f6..0a027c8 100644
--- a/modules/local/samtools_replaceheader.nf
+++ b/modules/local/samtools_replaceheader.nf
@@ -27,18 +27,18 @@ process SAMTOOLS_REHEADER {
     """
     # Replace SQ lines with those from external template
     ( samtools view --no-PG --header-only ${file} | \\
-    grep -v ^@SQ && grep ^@SQ ${header} ) > .temp.header.sam
+    grep -v ^@SQ && grep ^@SQ ${header} ) > temp.header.sam
 
     # custom sort for readability (retain order of insertion but sort groups by tag)
-    ( grep ^@HD .temp.header.sam || true && \
-    grep ^@SQ .temp.header.sam || true && \
-    grep ^@RG .temp.header.sam || true && \
-    grep ^@PG .temp.header.sam || true && \
-    grep -v -E '^@HD|^@SQ|^@RG|^@PG' .temp.header.sam || true; \
-    ) > .temp.sorted.header.sam
+    ( grep ^@HD temp.header.sam || true && \
+    grep ^@SQ temp.header.sam || true && \
+    grep ^@RG temp.header.sam || true && \
+    grep ^@PG temp.header.sam || true && \
+    grep -v -E '^@HD|^@SQ|^@RG|^@PG' temp.header.sam || true; \
+    ) > temp.sorted.header.sam
 
     # Insert new header into file
-    samtools reheader .temp.sorted.header.sam ${file} > ${prefix}.${suffix}
+    samtools reheader temp.sorted.header.sam ${file} > ${prefix}.${suffix}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":