fix tests

Author: priesgo

tests/run_test_6.sh

@@ -12,15 +12,15 @@ echo -e "single_sample\tnormal:"`pwd`"/test_data/TESTX_S1_L002.bam" >> test_data
 nextflow main.nf -profile test,conda --output $output_folder --input_bams test_data/test_bams.txt
 test -s $output_folder/single_sample/single_sample.normalized.vcf || { echo "Missing test 6 output file!"; exit 1; }
 test -s $output_folder/tumor_normal/tumor_normal.normalized.vcf || { echo "Missing test 6 output file!"; exit 1; }
-test -s $output_folder/single_sample/single_sample.normalized.vaf.vcf || { echo "Missing test 6 output file!"; exit 1; }
-test -s $output_folder/tumor_normal/tumor_normal.normalized.vaf.vcf || { echo "Missing test 6 output file!"; exit 1; }
-test -s $output_folder/single_sample/single_sample.normalized.vaf.filtered_multiallelics.vcf || { echo "Missing test 6 output file!"; exit 1; }
-test -s $output_folder/tumor_normal/tumor_normal.normalized.vaf.filtered_multiallelics.vcf || { echo "Missing test 6 output file!"; exit 1; }
+test -s $output_folder/single_sample/single_sample.vaf.vcf || { echo "Missing test 6 output file!"; exit 1; }
+test -s $output_folder/tumor_normal/tumor_normal.vaf.vcf || { echo "Missing test 6 output file!"; exit 1; }
+test -s $output_folder/single_sample/single_sample.filtered_multiallelics.vcf || { echo "Missing test 6 output file!"; exit 1; }
+test -s $output_folder/tumor_normal/tumor_normal.filtered_multiallelics.vcf || { echo "Missing test 6 output file!"; exit 1; }
 assert_eq `wc -l $output_folder/single_sample/single_sample.normalized.vcf | cut -d' ' -f 1` 53 "Wrong number of variants"
 assert_eq `wc -l $output_folder/tumor_normal/tumor_normal.normalized.vcf | cut -d' ' -f 1` 53 "Wrong number of variants"
 assert_eq `wc -l $output_folder/single_sample/single_sample.normalized.vaf.vcf | cut -d' ' -f 1` 72 "Wrong number of variants"
-assert_eq `grep tumor_af $output_folder/single_sample/single_sample.normalized.vaf.vcf | wc -l | cut -d' ' -f 1` 35 "Wrong number of variants"
-assert_eq `grep normal_af $output_folder/single_sample/single_sample.normalized.vaf.vcf | wc -l | cut -d' ' -f 1` 35 "Wrong number of variants"
-assert_eq `wc -l $output_folder/tumor_normal/tumor_normal.normalized.vaf.vcf | cut -d' ' -f 1` 60 "Wrong number of variants"
-assert_eq `wc -l $output_folder/tumor_normal/tumor_normal.normalized.vaf.filtered_multiallelics.vcf | cut -d' ' -f 1` 53 "Wrong number of variants"
-assert_eq `grep primary_af $output_folder/tumor_normal/tumor_normal.normalized.vaf.filtered_multiallelics.vcf | wc -l | cut -d' ' -f 1` 24 "Wrong number of variants"
+assert_eq `grep tumor_af $output_folder/single_sample/single_sample.vaf.vcf | wc -l | cut -d' ' -f 1` 35 "Wrong number of variants"
+assert_eq `grep normal_af $output_folder/single_sample/single_sample.vaf.vcf | wc -l | cut -d' ' -f 1` 35 "Wrong number of variants"
+assert_eq `wc -l $output_folder/tumor_normal/tumor_normal.vaf.vcf | cut -d' ' -f 1` 60 "Wrong number of variants"
+assert_eq `wc -l $output_folder/tumor_normal/tumor_normal.filtered_multiallelics.vcf | cut -d' ' -f 1` 53 "Wrong number of variants"
+assert_eq `grep primary_af $output_folder/tumor_normal/tumor_normal.filtered_multiallelics.vcf | wc -l | cut -d' ' -f 1` 24 "Wrong number of variants"

tests/run_test_7.sh

@@ -12,11 +12,11 @@ echo -e "single_sample\tnormal:"`pwd`"/test_data/TESTX_S1_L002.bam" >> test_data
 nextflow main.nf -profile test,conda --output $output_folder --input_bams test_data/test_bams.txt --skip_multiallelic_filter
 test -s $output_folder/single_sample/single_sample.normalized.vcf || { echo "Missing test 7 output file!"; exit 1; }
 test -s $output_folder/tumor_normal/tumor_normal.normalized.vcf || { echo "Missing test 7 output file!"; exit 1; }
-test -s $output_folder/single_sample/single_sample.normalized.vaf.vcf || { echo "Missing test 7 output file!"; exit 1; }
-test -s $output_folder/tumor_normal/tumor_normal.normalized.vaf.vcf || { echo "Missing test 7 output file!"; exit 1; }
+test -s $output_folder/single_sample/single_sample.vaf.vcf || { echo "Missing test 7 output file!"; exit 1; }
+test -s $output_folder/tumor_normal/tumor_normal.vaf.vcf || { echo "Missing test 7 output file!"; exit 1; }
 assert_eq `wc -l $output_folder/single_sample/single_sample.normalized.vcf | cut -d' ' -f 1` 53 "Wrong number of variants"
 assert_eq `wc -l $output_folder/tumor_normal/tumor_normal.normalized.vcf | cut -d' ' -f 1` 53 "Wrong number of variants"
-assert_eq `wc -l $output_folder/single_sample/single_sample.normalized.vaf.vcf | cut -d' ' -f 1` 72 "Wrong number of variants"
-assert_eq `grep tumor_af $output_folder/single_sample/single_sample.normalized.vaf.vcf | wc -l | cut -d' ' -f 1` 35 "Wrong number of variants"
-assert_eq `grep normal_af $output_folder/single_sample/single_sample.normalized.vaf.vcf | wc -l | cut -d' ' -f 1` 35 "Wrong number of variants"
-assert_eq `wc -l $output_folder/tumor_normal/tumor_normal.normalized.vaf.vcf | cut -d' ' -f 1` 60 "Wrong number of variants"
+assert_eq `wc -l $output_folder/single_sample/single_sample.vaf.vcf | cut -d' ' -f 1` 72 "Wrong number of variants"
+assert_eq `grep tumor_af $output_folder/single_sample/single_sample.vaf.vcf | wc -l | cut -d' ' -f 1` 35 "Wrong number of variants"
+assert_eq `grep normal_af $output_folder/single_sample/single_sample.vaf.vcf | wc -l | cut -d' ' -f 1` 35 "Wrong number of variants"
+assert_eq `wc -l $output_folder/tumor_normal/tumor_normal.vaf.vcf | cut -d' ' -f 1` 60 "Wrong number of variants"