From a69aebd01b0e37ffda790839c24c8b07f557514f Mon Sep 17 00:00:00 2001
From: MaxUlysse <max.u.garcia@gmail.com>
Date: Thu, 23 Jan 2020 10:19:00 +0100
Subject: [PATCH] fix index process

---
 tools/samtools/index/main.nf | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/tools/samtools/index/main.nf b/tools/samtools/index/main.nf
index acf1af41..7b065fa9 100644
--- a/tools/samtools/index/main.nf
+++ b/tools/samtools/index/main.nf
@@ -7,15 +7,14 @@ process samtools_index {
     path(bam)
 
     output:
-    path "*.sorted.bam"
+    path "*.bai"
 
     script:
     def suff_mem = ("${(task.memory.toBytes() - 6000000000) / task.cpus}" > 2000000000) ? 'true' : 'false'
     def avail_mem = (task.memory && suff_mem) ? "-m" + "${(task.memory.toBytes() - 6000000000) / task.cpus}" : ''
     """
-    samtools sort $bam \\
-        -@ ${task.cpus} ${avail_mem} \\
-        -o ${bam.baseName}.sorted.bam
+    samtools index $bam \\
+        -@ ${task.cpus} ${avail_mem}
 
     samtools --version &> v_samtools.txt
     """