From bbb99cb8d679555cc01c98766de7869f83283545 Mon Sep 17 00:00:00 2001
From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
Date: Mon, 29 Aug 2022 13:11:58 +0200
Subject: [PATCH] Fix/samtools flagstat (#1979)

* fix samtools stats thread usage

* flagstat: fix threads
---
 modules/samtools/flagstat/main.nf        | 4 ++--
 tests/modules/samtools/flagstat/test.yml | 2 +-
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/samtools/flagstat/main.nf b/modules/samtools/flagstat/main.nf
index 03ec2dcf..c3152aca 100644
--- a/modules/samtools/flagstat/main.nf
+++ b/modules/samtools/flagstat/main.nf
@@ -1,6 +1,6 @@
 process SAMTOOLS_FLAGSTAT {
     tag "$meta.id"
-    label 'process_low'
+    label 'process_single'
 
     conda (params.enable_conda ? "bioconda::samtools=1.15.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
@@ -23,7 +23,7 @@ process SAMTOOLS_FLAGSTAT {
     """
     samtools \\
         flagstat \\
-        --threads ${task.cpus-1} \\
+        --threads ${task.cpus} \\
         $bam \\
         > ${prefix}.flagstat
 
diff --git a/tests/modules/samtools/flagstat/test.yml b/tests/modules/samtools/flagstat/test.yml
index 31762434..4351a2b7 100644
--- a/tests/modules/samtools/flagstat/test.yml
+++ b/tests/modules/samtools/flagstat/test.yml
@@ -1,8 +1,8 @@
 - name: samtools flagstat test_samtools_flagstat
   command: nextflow run ./tests/modules/samtools/flagstat -entry test_samtools_flagstat -c ./tests/config/nextflow.config  -c ./tests/modules/samtools/flagstat/nextflow.config
   tags:
-    - samtools
     - samtools/flagstat
+    - samtools
   files:
     - path: output/samtools/test.flagstat
       md5sum: 4f7ffd1e6a5e85524d443209ac97d783