Fix/samtools flagstat (nf-core#1979)

* fix samtools stats thread usage * flagstat: fix threads
matthdsm · Aug 30, 2022 · 2f24e85 · 2f24e85
1 parent 595bd2e
commit 2f24e85
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Showing 2 changed files with 3 additions and 3 deletions.
diff --git 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
@@ -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