Commit c1241934 authored by VIENNE MAINA's avatar VIENNE MAINA
Browse files

Update host_filter.nf

parent f454f4e4
Pipeline #48509 skipped with stage
......@@ -25,10 +25,12 @@ process HOST_FILTER {
mkdir host_filter_flagstat
samtools flagstat ${sampleId}.bam > ${sampleId}.no_filter.flagstat
samtools flagstat ${sampleId}.without_host.bam >> host_filter_flagstat/${sampleId}.host_filter.flagstat
bamToFastq -i ${sampleId}.without_host.bam -fq cleaned_${sampleId}_R1.fastq -fq2 cleaned_${sampleId}_R2.fastq
samtools sort -n -o ${sampleId}.without_host_sort.bam ${sampleId}.without_host.bam
bamToFastq -i ${sampleId}.without_host_sort.bam -fq cleaned_${sampleId}_R1.fastq -fq2 cleaned_${sampleId}_R2.fastq
gzip cleaned_${sampleId}_R1.fastq
gzip cleaned_${sampleId}_R2.fastq
rm ${sampleId}.bam
rm ${sampleId}.without_host.bam
rm ${sampleId}.without_host_sort.bam
"""
}
\ No newline at end of file
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