haplotyper-battle-royale/modules/nanofilt/main.nf

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process NANOFILT {
cpus 1
memory '8.GB'
container 'quay.io/biocontainers/nanofilt:2.8.0--py_0'
input:
tuple val(prefix), path(reads)
output:
tuple val(prefix), path("*_trimmed.fastq.gz")
script:
"""
gzip \\
-cdf "${reads}" \\
| NanoFilt \\
--logfile "trimmed/${prefix}.nanofilt.log" \\
--length 100 \\
--quality 7 \\
--headcrop 30 \\
--tailcrop 30 \\
--minGC 0.1 \\
--maxGC 0.9 \\
| gzip \\
> "${prefix}_trimmed.fastq.gz"
"""
}