Fix bedtiools coverage in DSL1

Remove the `-sorted` flag so `bedtools` won't assume that the reference genome file is sorted.
IdoBar · Dec 12, 2023 · 3aa2ecc · 3aa2ecc
1 parent a2c9f87
commit 3aa2ecc
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/main.nf b/main.nf
@@ -2068,8 +2068,8 @@ process bedtools {
   samtools view -H ${bam} | grep '@SQ' | sed 's#@SQ\tSN:\\|LN:##g' > genome.txt
   
   ##  Run bedtools
-  bedtools coverage -nonamecheck -g genome.txt -sorted -a ${anno_file} -b ${bam} | pigz -p ${task.cpus - 1} > "${bam.baseName}".breadth.gz
-  bedtools coverage -nonamecheck -g genome.txt -sorted -a ${anno_file} -b ${bam} -mean | pigz -p ${task.cpus - 1} > "${bam.baseName}".depth.gz
+  bedtools coverage -nonamecheck -g genome.txt -a ${anno_file} -b ${bam} | pigz -p ${task.cpus - 1} > "${bam.baseName}".breadth.gz
+  bedtools coverage -nonamecheck -g genome.txt -a ${anno_file} -b ${bam} -mean | pigz -p ${task.cpus - 1} > "${bam.baseName}".depth.gz
   """
 }