fix tests

Author: priesgo

README.md

@@ -99,12 +99,12 @@ Purity values are in the range 0.0 to 1.0.
 The purity values are used to adjust the expected VAF which is then used to calculate the power to detect a 
 somatic mutation and the probability of an undetected somatic mutation.
 
-| Patient name       | Sample name:tumor purity            |
-|--------------------|-------------------------------------|
-| patient_1          | primary_tumor:0.4                   |
-| patient_1          | metastasis_tumor:0.5                |
-| patient_2          | primary_tumor:0.6                   |
-| patient_2          | metastasis_tumor:0.7                |
+| Patient name       | Sample name:purity   |
+|--------------------|----------------------|
+| patient_1          | primary_tumor:0.4    |
+| patient_1          | metastasis_tumor:0.5 |
+| patient_2          | primary_tumor:0.6    |
+| patient_2          | metastasis_tumor:0.7 |
 
 Each patient can have any number of samples. Any sample can have any number of BAM files, annotations from the 
 different BAM files of the same sample will be provided with suffixes _1, _2, etc.

tests/run_test_10.sh

@@ -3,13 +3,16 @@
 
 source tests/assert.sh
 output_folder=output/test10
+
 echo -e "tumor_normal\tprimary:"`pwd`"/test_data/TESTX_S1_L001.bam" > test_data/test_bams.txt
 echo -e "tumor_normal\tnormal:"`pwd`"/test_data/TESTX_S1_L002.bam" >> test_data/test_bams.txt
 echo -e "single_sample\ttumor:"`pwd`"/test_data/TESTX_S1_L001.bam" >> test_data/test_bams.txt
 echo -e "single_sample\ttumor:"`pwd`"/test_data/TESTX_S1_L002.bam" >> test_data/test_bams.txt
 echo -e "single_sample\tnormal:"`pwd`"/test_data/TESTX_S1_L001.bam" >> test_data/test_bams.txt
 echo -e "single_sample\tnormal:"`pwd`"/test_data/TESTX_S1_L002.bam" >> test_data/test_bams.txt
+
 nextflow main.nf -profile test,conda --output $output_folder --input_bams test_data/test_bams.txt --skip_normalization
+
 test -s $output_folder/single_sample/single_sample.filtered_multiallelics.vcf || { echo "Missing test 10 output file!"; exit 1; }
 test -s $output_folder/tumor_normal/tumor_normal.filtered_multiallelics.vcf || { echo "Missing test 10 output file!"; exit 1; }
 test -s $output_folder/single_sample/single_sample.vaf.vcf || { echo "Missing test 10 output file!"; exit 1; }

tests/run_test_6.sh

@@ -3,24 +3,31 @@
 
 source tests/assert.sh
 output_folder=output/test6
+
+
 echo -e "tumor_normal\tprimary:"`pwd`"/test_data/TESTX_S1_L001.bam" > test_data/test_bams.txt
 echo -e "tumor_normal\tnormal:"`pwd`"/test_data/TESTX_S1_L002.bam" >> test_data/test_bams.txt
 echo -e "single_sample\ttumor:"`pwd`"/test_data/TESTX_S1_L001.bam" >> test_data/test_bams.txt
 echo -e "single_sample\ttumor:"`pwd`"/test_data/TESTX_S1_L002.bam" >> test_data/test_bams.txt
 echo -e "single_sample\tnormal:"`pwd`"/test_data/TESTX_S1_L001.bam" >> test_data/test_bams.txt
 echo -e "single_sample\tnormal:"`pwd`"/test_data/TESTX_S1_L002.bam" >> test_data/test_bams.txt
+
+# run
 nextflow main.nf -profile test,conda --output $output_folder --input_bams test_data/test_bams.txt
+
+# check results
 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.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 -v '#' $output_folder/single_sample/single_sample.normalized.vcf | wc -l | cut -d' ' -f 1` 32 "Wrong number of variants"
+assert_eq `grep -v '#' $output_folder/tumor_normal/tumor_normal.normalized.vcf | wc -l | cut -d' ' -f 1` 32 "Wrong number of variants"
+assert_eq `grep -v '#' $output_folder/single_sample/single_sample.vaf.vcf | wc -l | cut -d' ' -f 1` 32 "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 -v '#' $output_folder/tumor_normal/tumor_normal.vaf.vcf | wc -l | cut -d' ' -f 1` 32 "Wrong number of variants"
+assert_eq `grep -v '#' $output_folder/tumor_normal/tumor_normal.filtered_multiallelics.vcf | wc -l | cut -d' ' -f 1` 23 "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

@@ -14,9 +14,9 @@ test -s $output_folder/single_sample/single_sample.normalized.vcf || { echo "Mis
 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.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.vaf.vcf | cut -d' ' -f 1` 72 "Wrong number of variants"
+assert_eq `grep -v '#' $output_folder/single_sample/single_sample.normalized.vcf | wc -l | cut -d' ' -f 1` 32 "Wrong number of variants"
+assert_eq `grep -v '#'  $output_folder/tumor_normal/tumor_normal.normalized.vcf | wc -l | cut -d' ' -f 1` 32 "Wrong number of variants"
+assert_eq `grep -v '#' $output_folder/single_sample/single_sample.vaf.vcf | wc -l | cut -d' ' -f 1` 32 "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 `grep -v '#' $output_folder/tumor_normal/tumor_normal.vaf.vcf | wc -l | cut -d' ' -f 1` 32 "Wrong number of variants"

tests/run_test_8.sh

@@ -3,20 +3,24 @@
 
 source tests/assert.sh
 output_folder=output/test8
+
 echo -e "tumor_normal\tprimary:"`pwd`"/test_data/TESTX_S1_L001.bam" > test_data/test_bams.txt
 echo -e "tumor_normal\tnormal:"`pwd`"/test_data/TESTX_S1_L002.bam" >> test_data/test_bams.txt
 echo -e "single_sample\ttumor:"`pwd`"/test_data/TESTX_S1_L001.bam" >> test_data/test_bams.txt
 echo -e "single_sample\ttumor:"`pwd`"/test_data/TESTX_S1_L002.bam" >> test_data/test_bams.txt
 echo -e "single_sample\tnormal:"`pwd`"/test_data/TESTX_S1_L001.bam" >> test_data/test_bams.txt
 echo -e "single_sample\tnormal:"`pwd`"/test_data/TESTX_S1_L002.bam" >> test_data/test_bams.txt
+
 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 8 output file!"; exit 1; }
 test -s $output_folder/tumor_normal/tumor_normal.normalized.vcf || { echo "Missing test 8 output file!"; exit 1; }
 test -s $output_folder/single_sample/single_sample.vaf.vcf || { echo "Missing test 8 output file!"; exit 1; }
 test -s $output_folder/tumor_normal/tumor_normal.vaf.vcf || { echo "Missing test 8 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.vaf.vcf | cut -d' ' -f 1` 72 "Wrong number of variants"
+
+assert_eq `grep -v '#' $output_folder/single_sample/single_sample.normalized.vcf | wc -l | cut -d' ' -f 1` 32 "Wrong number of variants"
+assert_eq `grep -v '#' $output_folder/tumor_normal/tumor_normal.normalized.vcf | wc -l | cut -d' ' -f 1` 32 "Wrong number of variants"
+assert_eq `grep -v '#' $output_folder/single_sample/single_sample.vaf.vcf | wc -l | cut -d' ' -f 1` 32 "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 `grep -v '#' $output_folder/tumor_normal/tumor_normal.vaf.vcf | wc -l | cut -d' ' -f 1` 32 "Wrong number of variants"

tests/run_test_9.sh

@@ -4,8 +4,11 @@
 source tests/assert.sh
 output_folder=output/test8
 snpeff_datadir=/home/you/snpeff
+
 nextflow main.nf -profile test,conda --output $output_folder --snpeff_organism hg19 --snpeff_datadir $snpeff_datadir
+
 test -s $output_folder/single_sample/single_sample.normalized.vcf || { echo "Missing test 1 output file!"; exit 1; }
 test -s $output_folder/tumor_normal/tumor_normal.normalized.vcf || { echo "Missing test 1 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 `grep -v '#' $output_folder/single_sample/single_sample.normalized.vcf | wc -l | cut -d' ' -f 1` 32 "Wrong number of variants"
+assert_eq `grep -v '#' $output_folder/tumor_normal/tumor_normal.normalized.vcf | wc -l | cut -d' ' -f 1` 32 "Wrong number of variants"