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Verified Commit 89474c57 authored by Laurent Modolo's avatar Laurent Modolo
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parasplit: fix parameters duplication

parent 8ead2e48
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......@@ -471,8 +471,8 @@ process {
}
withName: 'PARASPLIT' {
ext.output_for = { "${meta1.id}_${meta1.chunk}_${meta1.mates}_digested.fastq" }
ext.output_rev = { "${meta2.id}_${meta2.chunk}_${meta2.mates}_digested.fastq" }
ext.output_for = { "${meta1.id}_${meta1.chunk}_${meta1.mates}_digested.fastq.gz" }
ext.output_rev = { "${meta2.id}_${meta2.chunk}_${meta2.mates}_digested.fastq.gz" }
ext.args = { [
" --mode ${params.parasplit_mode}",
" --seed_size ${params.parasplit_seed}"
......
......@@ -18,7 +18,7 @@ process PARASPLIT {
def output_rev = task.ext.output_rev ?: "${meta2.id}_${meta2.chunk}_${meta2.mates}.fastq.gz"
"""
parasplit -sf ${reads1} -sr ${reads2} -le ${digestion} -of ${output_for} -or ${output_rev} -nt ${task.cpus} -sz 20 -m all ${args}
parasplit -sf ${reads1} -sr ${reads2} -le ${digestion} -of ${output_for} -or ${output_rev} -nt ${task.cpus} ${args}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
parasplit: \$(parasplit --version)
......
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