Merge pull request #9 from TRON-Bioinformatics/optional-gnomad

includes --args_filter in the tests
TRON-Bioinformatics · May 30, 2022 · e6a5305 · e6a5305
2 parents eabdca2 + 253336a
commit e6a5305
Showing 1 changed file with 1 addition and 1 deletion.
diff --git a/tests/test_09.sh b/tests/test_09.sh
@@ -5,6 +5,6 @@ source bin/assert.sh
 output=output/test9
 
 echo -e "sample_name\t"`pwd`"/test_data/SRR8244887.preprocessed.downsampled.bam\t"`pwd`"/test_data/SRR8244836.preprocessed.downsampled.bam" > test_data/test_input.txt
-nextflow main.nf -profile test,conda --output $output --input_files test_data/test_input.txt --gnomad false
+nextflow main.nf -profile test,conda --output $output --input_files test_data/test_input.txt --gnomad false  --args_filter "--contamination-estimate 0.2"
 
 test -s $output/sample_name/sample_name.mutect2.vcf || { echo "Missing output VCF file!"; exit 1; }