nf-core_modules/modules/snippy/core/main.nf

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process SNIPPY_CORE {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::snippy=4.6.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/snippy:4.6.0--hdfd78af_2':
'quay.io/biocontainers/snippy:4.6.0--hdfd78af_1' }"
input:
tuple val(meta), path(vcf), path(aligned_fa)
path reference
output:
tuple val(meta), path("${prefix}.aln") , emit: aln
tuple val(meta), path("${prefix}.full.aln"), emit: full_aln
tuple val(meta), path("${prefix}.tab") , emit: tab
tuple val(meta), path("${prefix}.vcf") , emit: vcf
tuple val(meta), path("${prefix}.txt") , emit: txt
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
def is_compressed = reference.getName().endsWith(".gz") ? true : false
def reference_name = reference.getName().replace(".gz", "")
"""
if [ "$is_compressed" == "true" ]; then
gzip -c -d $reference > $reference_name
fi
# Collect samples into necessary folders
mkdir samples
find . -name "*.vcf" | sed 's/.vcf//' | xargs -I {} bash -c 'mkdir samples/{}'
find . -name "*.vcf" | sed 's/.vcf//' | xargs -I {} bash -c 'cp -L {}.vcf samples/{}/{}.vcf'
find . -name "*.aligned.fa" | sed 's/.aligned.fa//' | xargs -I {} bash -c 'cp -L {}.aligned.fa samples/{}/{}.aligned.fa'
# Run snippy-core
snippy-core \\
$args \\
--ref $reference_name \\
--prefix $prefix \\
samples/*
cat <<-END_VERSIONS > versions.yml
"${task.process}":
snippy-core: \$(echo \$(snippy-core --version 2>&1) | sed 's/snippy-core //')
END_VERSIONS
"""
}