nf-core_modules/tools/shovill/main.nf

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2020-03-05 09:29:23 +00:00
process shovill {
tag { shovill }
publishDir "${params.outdir}", pattern: '*.fasta', mode: 'copy'
container "quay.io/biocontainers/shovill:1.0.9--0"
input:
tuple(sample_id, path(forward), path(reverse))
output:
path("${sample_id}.fasta")
script:
"""
shovill --R1 ${forward} --R2 ${reverse} --outdir shovill_out
mv shovill_out/contigs.fa ${sample_id}.fasta
"""
}