simplified tests without singularity

SciLifeLab · Sep 13, 2018 · 72c0c2c · 72c0c2c
1 parent 39fdfd4
commit 72c0c2c
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Showing 2 changed files with 9 additions and 20 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -11,14 +11,12 @@ env:
   global:
     - NXF_VER=0.31.0 SGT_VER=2.5.1
   matrix:
-    - CE=singularity TEST=SOMATIC
     - CE=docker      TEST=SOMATIC
     - CE=docker      TEST=ANNOTATEVEP
-    - CE=singularity TEST=ANNOTATESNPEFF
     - CE=docker      TEST=ANNOTATESNPEFF
-    - CE=singularity TEST=GERMLINE
     - CE=docker      TEST=GERMLINE
 
+
 install:
   # Install Nextflow (and Singularity if needed)
   - "./scripts/install.sh --engine $CE"

diff --git a/scripts/test.sh b/scripts/test.sh
@@ -89,33 +89,24 @@ then
   fi
 fi
 
+
 if [[ ALL,GERMLINE =~ $TEST ]]
 then
 	# Added Strelka to germline test (no Strelka best practices test for this small data) and not asking for reports
-	echo "###########################   TESTING GERMLINE WGS ########################################"
-  run_wrapper --germline --sampleDir Sarek-data/testdata/tiny/normal --variantCalling --tools HaplotypeCaller,Strelka --noReports
-	# testing targeted calls
-	echo "###########################   TESTING GERMLINE TARGETED ########################################"
-  run_wrapper --germline --sampleDir Sarek-data/testdata/tiny/normal --variantCalling --tools HaplotypeCaller,Strelka --bed `pwd`/Sarek-data/testdata/target.bed --noReports
-	echo "###########################   TESTING GERMLINE RECALIBRATION ########################################"
-  run_wrapper --germline --step recalibrate --noReports
-  clean_repo
+	run_wrapper --germline --sampleDir Sarek-data/testdata/tiny/normal --variantCalling --tools HaplotypeCaller,Strelka
+	run_wrapper --germline --sampleDir Sarek-data/testdata/tiny/normal --variantCalling --tools HaplotypeCaller,Strelka --bed `pwd`/Sarek-data/testdata/target.bed --noReports
+	run_wrapper --germline --step recalibrate --noReports
+	clean_repo
 fi
 
 if [[ ALL,SOMATIC =~ $TEST ]]
 then
-	# Do we need HaplotypeCaller in the somatic test?
-	echo "###########################   TESTING SOMATIC FROM SCRATCH ########################################"
 	run_wrapper --somatic --sample Sarek-data/testdata/tsv/tiny-manta.tsv --variantCalling --tools FreeBayes,HaplotypeCaller,Manta,Mutect2 --noReports
-	echo "###########################   TESTING SOMATIC STRELKA BEST PRACTICE FROM SCRATCH ########################################"
-  run_wrapper --somatic --sample Sarek-data/testdata/tsv/tiny-manta.tsv --variantCalling --tools Manta,Strelka --noReports --strelkaBP
-	# run targeted tests with tiny set
-	echo "###########################   TESTING SOMATIC TARGETED  ########################################"
-  run_wrapper --somatic --sample  Sarek-data/testdata/tsv/tiny.tsv --variantCalling --tools FreeBayes,HaplotypeCaller,Mutect2,Strelka --bed `pwd`/Sarek-data/testdata/target.bed
-  clean_repo
+	run_wrapper --somatic --sample Sarek-data/testdata/tsv/tiny-manta.tsv --variantCalling --tools Manta,Strelka --noReports --strelkaBP
+	run_wrapper --somatic --sample Sarek-data/testdata/tsv/tiny.tsv --variantCalling --tools FreeBayes,HaplotypeCaller,Mutect2,Strelka --bed `pwd`/Sarek-data/testdata/target.bed
+	clean_repo
 fi
 
-
 if [[ ALL,ANNOTATEALL,ANNOTATESNPEFF,ANNOTATEVEP =~ $TEST ]]
 then
   if [[ $TEST = ANNOTATESNPEFF ]]