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Verified Commit a433d102 authored by Laurent Modolo's avatar Laurent Modolo
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minimap2: fix single-end handling

parent e90c027d
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......@@ -56,7 +56,7 @@ process mapping_fastq {
minimap2 ${params.mapping_fastq} -t ${task.cpus} -K ${memory} ${fasta} ${reads[0]} ${reads[1]} |
samtools view -Sb - > ${pair_id}.bam
"""
else if (reads.size() == 1)
else
"""
minimap2 ${params.mapping_fastq} -t ${task.cpus} -K ${memory} ${fasta} ${reads} |
samtools view -Sb - > ${pair_id}.bam
......
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