fix BAMQC output

CHANGELOG.md

@@ -33,6 +33,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 ### `Fixed`
 -   [#720](https://github.com/SciLifeLab/Sarek/pull/720) - bamQC is now run on the recalibrated bams, and not after MarkDuplicates
 -   [#726](https://github.com/SciLifeLab/Sarek/pull/726) - Fix Ascat ref file input (one file can't be a set)
+-   [#727](https://github.com/SciLifeLab/Sarek/pull/727) - bamQC outputs are no longer overwritten (name of dir is now the file instead of sample)
 
 ## [2.2.2] - 2018-12-19
 

main.nf

@@ -190,7 +190,7 @@ process RunBamQCmapped {
     set idPatient, status, idSample, idRun, file(bam) from mappedBamForQC
 
   output:
-    file(idSample) into bamQCmappedReport
+    file("${bam.baseName}") into bamQCmappedReport
 
   when: !params.noReports && !params.noBAMQC
 
@@ -204,7 +204,7 @@ process RunBamQCmapped {
   -nt ${task.cpus} \
   -skip-duplicated \
   --skip-dup-mode 0 \
-  -outdir ${idSample} \
+  -outdir ${bam.baseName} \
   -outformat HTML
   """
 }
@@ -459,7 +459,7 @@ process RunBamQCrecalibrated {
     set idPatient, status, idSample, file(bam), file(bai) from bamForBamQC
 
   output:
-    file(idSample) into bamQCrecalibratedReport
+    file("${bam.baseName}") into bamQCrecalibratedReport
 
   when: !params.noReports && !params.noBAMQC
 
@@ -473,7 +473,7 @@ process RunBamQCrecalibrated {
   -nt ${task.cpus} \
   -skip-duplicated \
   --skip-dup-mode 0 \
-  -outdir ${idSample} \
+  -outdir ${bam.baseName} \
   -outformat HTML
   """
 }