From a2bd6a6787b7bd773760cce49ccc95051176e918 Mon Sep 17 00:00:00 2001 From: Pablo Riesgo Ferreiro Date: Mon, 22 Nov 2021 13:43:34 +0100 Subject: [PATCH] fix test --- tests/run_test_7.sh | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/tests/run_test_7.sh b/tests/run_test_7.sh index 870e6af..046e8cb 100644 --- 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; }