Remove default filters in mpileup as well...

merszym · merszym · commit b418acbcfabf · 2024-11-19T14:29:30.000+01:00
diff --git a/conf/process.config b/conf/process.config
@@ -144,7 +144,7 @@ process {
     }
 
     withName:"SAMTOOLS_MPILEUP" {
-        ext.args = "--output-BP-5 --no-output-ends --no-output-ins --no-output-del --no-output-ins --no-output-del --min-BQ 0  -R"
+        ext.args = "--output-BP-5 --no-output-ends --no-output-ins --no-output-del --no-output-ins --no-output-del --min-BQ 0  -R --ff 0"
         publishDir = [
             [
                 path: "${outdir}/out",

Original file line number	Diff line number	Diff line change
`@@ -144,7 +144,7 @@ process {`
`144`	`144`	`}`
`145`	`145`
`146`	`146`	`withName:"SAMTOOLS_MPILEUP" {`
`147`		`- ext.args = "--output-BP-5 --no-output-ends --no-output-ins --no-output-del --no-output-ins --no-output-del --min-BQ 0 -R"`
	`147`	`+ ext.args = "--output-BP-5 --no-output-ends --no-output-ins --no-output-del --no-output-ins --no-output-del --min-BQ 0 -R --ff 0"`
`148`	`148`	`publishDir = [`
`149`	`149`	`[`
`150`	`150`	`path: "${outdir}/out",`