fix tests

Author: priesgo

Makefile

@@ -29,3 +29,4 @@ test:
 	bash test/scripts/run_test_11.sh
 	bash test/scripts/run_test_12.sh
 	bash test/scripts/run_test_13.sh
+	bash test/scripts/run_test_14.sh

test/scripts/run_test_14.sh

@@ -1,18 +1,16 @@
 #!/bin/bash
 
 
-source tests/assert.sh
-output_folder=output/test11
-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 --phasing_sample normal
-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; }
+source test/scripts/assert.sh
+output_folder=test/output/test14
+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 \
+  --phasing_sample normal --input_vcfs test/data/test_input_single_sample.txt
+
 test -s $output_folder/single_sample/single_sample.phased.vcf || { echo "Missing test 10 output file!"; exit 1; }
-test -s $output_folder/tumor_normal/tumor_normal.vaf.vcf || { echo "Missing test 10 output file!"; exit 1; }
-test -s $output_folder/tumor_normal/tumor_normal.phased.vcf || { echo "Missing test 10 output file!"; exit 1; }