From f0a86eaf5bf6ca73c5571193edd00c25bfa308f5 Mon Sep 17 00:00:00 2001
From: Matthieu Muffato <mm49@sanger.ac.uk>
Date: Mon, 26 Sep 2022 17:44:36 +0100
Subject: [PATCH] Multithreaded samtools commands (#2080)

* Multithreaded samtools commands

* Updated the checksums since the BAM files include the actual command line

Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com>
---
 modules/samtools/ampliconclip/main.nf        |  1 +
 modules/samtools/depth/main.nf               |  1 +
 modules/samtools/idxstats/main.nf            |  1 +
 tests/modules/samtools/ampliconclip/test.yml | 12 ++++++------
 4 files changed, 9 insertions(+), 6 deletions(-)

diff --git a/modules/samtools/ampliconclip/main.nf b/modules/samtools/ampliconclip/main.nf
index 2b90c953..3a3bb852 100644
--- a/modules/samtools/ampliconclip/main.nf
+++ b/modules/samtools/ampliconclip/main.nf
@@ -31,6 +31,7 @@ process SAMTOOLS_AMPLICONCLIP {
     """
     samtools \\
         ampliconclip \\
+        --threads ${task.cpus-1} \\
         $args \\
         $rejects \\
         $stats \\
diff --git a/modules/samtools/depth/main.nf b/modules/samtools/depth/main.nf
index e508a5f7..d5f2ba60 100644
--- a/modules/samtools/depth/main.nf
+++ b/modules/samtools/depth/main.nf
@@ -23,6 +23,7 @@ process SAMTOOLS_DEPTH {
     """
     samtools \\
         depth \\
+        --threads ${task.cpus-1} \\
         $args \\
         -o ${prefix}.tsv \\
         $bam
diff --git a/modules/samtools/idxstats/main.nf b/modules/samtools/idxstats/main.nf
index 4b245419..87618e5f 100644
--- a/modules/samtools/idxstats/main.nf
+++ b/modules/samtools/idxstats/main.nf
@@ -24,6 +24,7 @@ process SAMTOOLS_IDXSTATS {
     """
     samtools \\
         idxstats \\
+        --threads ${task.cpus-1} \\
         $bam \\
         > ${prefix}.idxstats
 
diff --git a/tests/modules/samtools/ampliconclip/test.yml b/tests/modules/samtools/ampliconclip/test.yml
index cfc10dd1..dd9fdbb7 100644
--- a/tests/modules/samtools/ampliconclip/test.yml
+++ b/tests/modules/samtools/ampliconclip/test.yml
@@ -5,7 +5,7 @@
     - samtools/ampliconclip
   files:
     - path: output/samtools/test.bam
-      md5sum: d270363a7fb3d96be2df211099efc75b
+      md5sum: 69e4ba713447864231f6cbbaf036c51d
 
 - name: samtools ampliconclip no stats with rejects
   command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_no_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config
@@ -14,9 +14,9 @@
     - samtools/ampliconclip
   files:
     - path: output/samtools/test.bam
-      md5sum: e7c4e64c259212e1670f6de96a5549b4
+      md5sum: dd2ed9d7cc4ddc070ece2dccc577f94b
     - path: output/samtools/test.cliprejects.bam
-      md5sum: b7c057b11950c2271a0c92236bee94b7
+      md5sum: 7d641f6da838f41d75eaabbd897f60bd
 
 - name: samtools ampliconclip with stats with rejects
   command: nextflow run ./tests/modules/samtools/ampliconclip -entry test_samtools_ampliconclip_with_stats_with_rejects -c ./tests/config/nextflow.config -c ./tests/modules/samtools/ampliconclip/nextflow.config
@@ -25,8 +25,8 @@
     - samtools/ampliconclip
   files:
     - path: output/samtools/test.bam
-      md5sum: e75992d4ff69cbaed9a089231be86b5e
+      md5sum: 6c19afc0873fba2f4e530eabf61c0735
     - path: output/samtools/test.cliprejects.bam
-      md5sum: 729f03e7a2801d2c56c32bef8f3d6ead
+      md5sum: 1dfb61aa80d8e90add324ed61ed17061
     - path: output/samtools/test.clipstats.txt
-      md5sum: fc23355e1743d47f2541f2cb1a7a0cda
+      md5sum: 05ead360a98fab6a678056e326c4f1f3