Format subsampling

genepi · Mar 7, 2024 · 7e79495 · 7e79495
1 parent f2d760c
commit 7e79495
Showing 1 changed file with 3 additions and 0 deletions.
diff --git a/modules/local/subsampling.nf b/modules/local/subsampling.nf
@@ -12,10 +12,13 @@ process SUBSAMPLING {
     samtools coverage ${bam_file} > samtools_coverage_${bam_file.baseName}.txt
     csvtk grep -t -f3 -p 16569 -C '\$' samtools_coverage_${bam_file.baseName}.txt
     mean_cov=\$(csvtk grep -t -f3 -p 16569 -C '\$' samtools_coverage_${bam_file.baseName}.txt | csvtk cut -t -f 7)
+    
     # convert to integer
     mean_cov_int=\$(printf "%.0f" "\$mean_cov")
+    
     # set seed to 1 (for reproducbility) and FRAC to coverage/mean_cov (e.g. 1.2)
     fraction=\$(echo "scale=4; 1+(${coverage} / \${mean_cov})" | bc)
+    
     if [ \${mean_cov_int} -gt ${coverage} ]
     then
         samtools view -s \$fraction -b -o ${bam_file.baseName}.subsampled.bam ${bam_file}