From e904107c22d53b99c73114b7c1577924786f9d43 Mon Sep 17 00:00:00 2001
From: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
Date: Thu, 16 Sep 2021 10:23:07 +0200
Subject: [PATCH] Chromap patch (#712)

* Initialise chromap module

* Revert "Initialise chromap module"

This reverts commit 47c67ae231a6f221ef5b9b7b444b583b5406852b.

* Remove samtools version

* Add space

* Remove whitespace
---
 modules/chromap/chromap/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/chromap/chromap/main.nf b/modules/chromap/chromap/main.nf
index 330ba60e..be60c6bd 100644
--- a/modules/chromap/chromap/main.nf
+++ b/modules/chromap/chromap/main.nf
@@ -64,8 +64,6 @@ process CHROMAP_CHROMAP {
         samtools view $options.args2 -@ ${task.cpus} -bh \\
             -o ${prefix}.bam ${prefix}.${file_extension}
         rm ${prefix}.${file_extension}
-
-        samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
         """
     }
     if (meta.single_end) {
@@ -76,6 +74,7 @@ process CHROMAP_CHROMAP {
             -r $fasta \\
             -1 ${reads.join(',')} \\
             -o ${prefix}.${file_extension}
+
         echo "$VERSION" > ${software}.version.txt
         """ + compression_cmds
     } else {
@@ -87,6 +86,7 @@ process CHROMAP_CHROMAP {
             -1 ${reads[0]} \\
             -2 ${reads[1]} \\
             -o ${prefix}.${file_extension}
+
         echo "$VERSION" > ${software}.version.txt
         """ + compression_cmds
     }