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Rename output channel

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drpatelh 2021-02-09 23:26:18 +00:00
parent 6765db81be
commit 6795fe04b8
1 changed files with 6 additions and 6 deletions
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12
software/pangolin/main.nf
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@ -11,19 +11,19 @@ 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=2.1.7=py_0' : null) conda (params.enable_conda ? 'bioconda::pangolin=2.2.1=py_0' : 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:2.1.7--py_0' container 'https://depot.galaxyproject.org/singularity/pangolin:2.2.1--py_0'
} else { } else {
container 'quay.io/biocontainers/pangolin:2.1.7--py_0' container 'quay.io/biocontainers/pangolin:2.2.1--py_0'
} }
input: input:
tuple val(meta), path(fasta) tuple val(meta), path(fasta)
output: output:
tuple val(meta), path('*.lineage_report.csv'), emit: report tuple val(meta), path('*.csv'), emit: report
path '*.version.txt' , emit: version path '*.version.txt' , emit: version
script: script:
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
@ -31,7 +31,7 @@ process PANGOLIN {
""" """
pangolin \\ pangolin \\
$fasta\\ $fasta\\
--outfile ${prefix}.lineage_report.csv \\ --outfile ${prefix}.pangolin.csv \\
$options.args $options.args
pangolin --version | sed "s/pangolin //g" > ${software}.version.txt pangolin --version | sed "s/pangolin //g" > ${software}.version.txt