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Fix typo (#1586)

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Lauri Mesilaakso 2022-04-29 09:37:23 +02:00 committed by GitHub
parent ec10f98d55
commit 1a5a9e7b40
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1 changed files with 2 additions and 2 deletions
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modules/minimap2/align/main.nf
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@ -27,8 +27,8 @@ process MINIMAP2_ALIGN {
def prefix = task.ext.prefix ?: "${meta.id}" def prefix = task.ext.prefix ?: "${meta.id}"
def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}" def input_reads = meta.single_end ? "$reads" : "${reads[0]} ${reads[1]}"
def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf" def bam_output = bam_format ? "-a | samtools sort | samtools view -@ ${task.cpus} -b -h -o ${prefix}.bam" : "-o ${prefix}.paf"
def cigar_paf = cigar_paf_format && !sam_format ? "-c" : '' def cigar_paf = cigar_paf_format && !bam_format ? "-c" : ''
def set_cigar_bam = cigar_bam && sam_format ? "-L" : '' def set_cigar_bam = cigar_bam && bam_format ? "-L" : ''
""" """
minimap2 \\ minimap2 \\
$args \\ $args \\