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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
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Kevin Menden 2021-01-29 12:33:37 +01:00 committed by GitHub
parent 14ade8060f
commit 8f2f936cd4
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2 changed files with 7 additions and 7 deletions
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10
software/pangolin/main.nf
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@ -19,10 +19,10 @@ process PANGOLIN {
} }
input: input:
tuple val(meta), path(assembly) tuple val(meta), path(fasta)
output: output:
tuple val(meta), path('*.lineage_report.csv') , emit: lineage tuple val(meta), path('*.lineage_report.csv'), emit: report
path '*.version.txt' , emit: version path '*.version.txt' , emit: version
script: script:
@ -30,9 +30,9 @@ process PANGOLIN {
def prefix = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}.${options.suffix}" : "${meta.id}"
""" """
pangolin \\ pangolin \\
$assembly \\ $fasta\\
--outfile ${prefix}.lineage_report.csv \\ --outfile ${prefix}.lineage_report.csv \\
$options.args $options.args
pangolin --version | sed "s/pangolin //g" > ${software}.version.txt pangolin --version | sed "s/pangolin //g" > ${software}.version.txt
""" """

4
software/pangolin/meta.yml
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@ -37,13 +37,13 @@ input:
type: map type: map
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
- assembly: - fasta:
type: file type: file
description: | description: |
The virus genome assembly to be evaluated The virus genome assembly to be evaluated
output: output:
- lineage_report: - report:
type: file type: file
description: The lineage report description: The lineage report
pattern: "{prefix}.lineage_report.csv" pattern: "{prefix}.lineage_report.csv"