fix test

TRON-Bioinformatics · Nov 22, 2021 · a2bd6a6 · a2bd6a6
1 parent a2a152f
commit a2bd6a6
Showing 1 changed file with 6 additions and 2 deletions.
diff --git a/tests/run_test_7.sh b/tests/run_test_7.sh
@@ -3,8 +3,12 @@
 
 source tests/assert.sh
 output_folder=output/test7
-echo -e "tumor_normal\t"`pwd`"/test_data/TESTX_S1_L001.bam\t"`pwd`"/test_data/TESTX_S1_L002.bam" > test_data/test_bams.txt
-echo -e "single_sample\t"`pwd`"/test_data/TESTX_S1_L001.bam,"`pwd`"/test_data/TESTX_S1_L002.bam\t"`pwd`"/test_data/TESTX_S1_L001.bam,"`pwd`"/test_data/TESTX_S1_L002.bam" >> test_data/test_bams.txt
+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_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; }