remove the paired flag from the bamfile after filtering

Author: merszym

CHANGELOG.md

@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
   - Changes the `bam_deam_stats.py` and the `mask_deamination.py` scripts to look at 3' G to A substitutions instead of the C to T changes as done before.
   - Nothing changes for default runs
 - Fix a bug in the processing of paired fastq-files.
+  - removes the "1" flag from the resulting bam files (make sure to merge your reads before quicksand!)
 
 ## [v2.1] - 2024-03-21
 

conf/process.config

@@ -25,9 +25,12 @@ process {
     //
     // Workflow: Bamfilter
     //
+    //
+    // remove the paired information after filtering.
+    // IF people dont merge their reads, that causes downstream problems, so this is necessary.
 
     withName: "SAMTOOLS_FILTER" {
-        ext.args = "-F ${params.bamfilterflag}"
+        ext.args = "-F ${params.bamfilterflag} --remove-flags 1"
     }
 
     withName: "BAM_LENGTHFILTER" {