Merge pull request #15 from Juke34/eascarrunz-patch-1

eascarrunz · web-flow · commit 633ca01d318c · 2025-05-28T17:08:15.000+02:00
reduce pool size to avoid OOM problems
diff --git a/modules/bamutil.nf b/modules/bamutil.nf
@@ -13,7 +13,7 @@ process bamutil_clipoverlap {
     script:
 
         """
-        bam clipOverlap --storeOrig CG --poolSize 50000000 --in ${bam} --out ${bam}_clipoverlap.bam --stats > ${meta.id}_bamutil_clipoverlap.log
+        bam clipOverlap --storeOrig CG --poolSize 5000000 --in ${bam} --out ${bam}_clipoverlap.bam --stats > ${meta.id}_bamutil_clipoverlap.log
         """
 
 }

Original file line number	Diff line number	Diff line change
`@@ -13,7 +13,7 @@ process bamutil_clipoverlap {`
`13`	`13`	`script:`
`14`	`14`
`15`	`15`	`"""`
`16`		`- bam clipOverlap --storeOrig CG --poolSize 50000000 --in ${bam} --out ${bam}_clipoverlap.bam --stats > ${meta.id}_bamutil_clipoverlap.log`
	`16`	`+ bam clipOverlap --storeOrig CG --poolSize 5000000 --in ${bam} --out ${bam}_clipoverlap.bam --stats > ${meta.id}_bamutil_clipoverlap.log`
`17`	`17`	`"""`
`18`	`18`
`19`	`19`	`}`