Merge remote-tracking branch 'upstream/dev' into 2.6.1

nf-core · Jun 23, 2020 · e6b97db · e6b97db
2 parents 2860623 + ff2ac6a
commit e6b97db
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Showing 2 changed files with 8 additions and 4 deletions.
diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml
@@ -1,6 +1,6 @@
-name: nf-core AWS test
+name: nf-core AWS full test
 # This workflow is triggered on push to the master branch and on published releases.
-# It runs the -profile 'test' on AWS batch
+# It runs the -profile 'test_full' on AWS batch
 
 on:
   release:

diff --git a/main.nf b/main.nf
@@ -2705,8 +2705,8 @@ process FilterMutect2Calls {
         file(germlineResource) from ch_germline_resource
         file(germlineResourceIndex) from ch_germline_resource_tbi
         file(intervals) from ch_intervals
-      
-                  output:
+
+    output:
         set val("Mutect2"), idPatient, idSamplePair, file("Mutect2_filtered_${idSamplePair}.vcf.gz"), file("Mutect2_filtered_${idSamplePair}.vcf.gz.tbi"), file("Mutect2_filtered_${idSamplePair}.vcf.gz.filteringStats.tsv") into filteredMutect2Output
 
     when: 'mutect2' in tools
@@ -3382,6 +3382,10 @@ controlFreecVizOut.dump(tag:'ControlFreecViz')
 (vcfMantaSomaticSV, vcfMantaDiploidSV) = vcfManta.into(2)
 
 vcfKeep = Channel.empty().mix(
+    filteredMutect2Output.map{
+        variantCaller, idPatient, idSample, vcf, tbi, tsv ->
+        [variantcaller, idSample, vcf]
+    },
     vcfConcatenated.map{
         variantcaller, idPatient, idSample, vcf, tbi ->
         [variantcaller, idSample, vcf]