Commit a7d813f5 authored by Anthony Fullam's avatar Anthony Fullam 🇮🇪
Browse files

[BUGFIX] Wrong name of singles fastq.

parent 846d831f
......@@ -125,7 +125,7 @@ process alignment {
fi
else
READS=single_end
bowtie2 -X 1000 -p 24 -x ${params.reference} -U ${sample_id}.single.fq.gz | samtools view -hb -u -F 4 - | samtools sort -m 8G -@4 > ${sample_id}.bam
bowtie2 -X 1000 -p 24 -x ${params.reference} -U ${sample_id}.singles.fq.gz | samtools view -hb -u -F 4 - | samtools sort -m 8G -@4 > ${sample_id}.bam
fi
mkdir logs
cp .command.log logs/${sample_id}.bowtie.log
......
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