From 0218824b860979b7c62bcf3159c7288aa222861a Mon Sep 17 00:00:00 2001
From: Kevin Menden <kevin.menden@t-online.de>
Date: Wed, 10 Mar 2021 09:02:23 +0100
Subject: [PATCH] add task.cpus to pangolin (#263)

* add task.cpus to pangolin

* bumped pangolin to v2.3.2
---
 software/pangolin/main.nf        | 7 ++++---
 tests/software/pangolin/test.yml | 2 +-
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/software/pangolin/main.nf b/software/pangolin/main.nf
index a2ff935f..23227eb9 100644
--- a/software/pangolin/main.nf
+++ b/software/pangolin/main.nf
@@ -11,11 +11,11 @@ process PANGOLIN {
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    conda (params.enable_conda ? 'bioconda::pangolin=2.2.2' : null)
+    conda (params.enable_conda ? 'bioconda::pangolin=2.3.2' : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container 'https://depot.galaxyproject.org/singularity/pangolin:2.2.2--py_0'
+        container 'https://depot.galaxyproject.org/singularity/pangolin:2.3.2--py_0'
     } else {
-        container 'quay.io/biocontainers/pangolin:2.2.2--py_0'
+        container 'quay.io/biocontainers/pangolin:2.3.2--py_0'
     }
 
     input:
@@ -32,6 +32,7 @@ process PANGOLIN {
     pangolin \\
         $fasta\\
         --outfile ${prefix}.pangolin.csv \\
+        --threads $task.cpus \\
         $options.args
 
     pangolin --version | sed "s/pangolin //g" > ${software}.version.txt
diff --git a/tests/software/pangolin/test.yml b/tests/software/pangolin/test.yml
index 44074f09..494c057e 100644
--- a/tests/software/pangolin/test.yml
+++ b/tests/software/pangolin/test.yml
@@ -4,4 +4,4 @@
     - pangolin
   files:
     - path: ./output/pangolin/test.pangolin.csv
-      md5sum: 43edd267815f6408b66961a0abf9ddd6
+      md5sum: 1d513775cec0901ebee1359c91035d3a