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add task.cpus to pangolin (#263)

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* add task.cpus to pangolin

* bumped pangolin to v2.3.2
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Kevin Menden 2021-03-10 09:02:23 +01:00 committed by GitHub
parent a552d97849
commit 0218824b86
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GPG key ID: 4AEE18F83AFDEB23
2 changed files with 5 additions and 4 deletions
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7
software/pangolin/main.nf
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@ -11,11 +11,11 @@ process PANGOLIN {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } 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) { 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 { } else {
container 'quay.io/biocontainers/pangolin:2.2.2--py_0' container 'quay.io/biocontainers/pangolin:2.3.2--py_0'
} }
input: input:
@ -32,6 +32,7 @@ process PANGOLIN {
pangolin \\ pangolin \\
$fasta\\ $fasta\\
--outfile ${prefix}.pangolin.csv \\ --outfile ${prefix}.pangolin.csv \\
--threads $task.cpus \\
$options.args $options.args
pangolin --version | sed "s/pangolin //g" > ${software}.version.txt pangolin --version | sed "s/pangolin //g" > ${software}.version.txt

2
tests/software/pangolin/test.yml
View file

@ -4,4 +4,4 @@
- pangolin - pangolin
files: files:
- path: ./output/pangolin/test.pangolin.csv - path: ./output/pangolin/test.pangolin.csv
md5sum: 43edd267815f6408b66961a0abf9ddd6 md5sum: 1d513775cec0901ebee1359c91035d3a