Update host_filter.nf

modules/host_filter.nf

@@ -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
     """
 }
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