diff --git a/src/lofreq/call/test.sh b/src/lofreq/call/test.sh index e69de29b..ccd8100c 100644 --- a/src/lofreq/call/test.sh +++ b/src/lofreq/call/test.sh @@ -0,0 +1,17 @@ +#!/bin/bash + +set -e + +dir_in="${meta_resources_dir%/}/test_data" + +echo "> Run lofreq call" +"$meta_executable" \ + --input "$dir_in/a.bam" \ + --input_bai "$dir_in/a.bai" \ + --ref "$dir_in/genome.fasta" \ + --output "output.vcf" \ + +echo ">> Checking output" +[ ! -f "output.vcf" ] && echo "Output file output.vcf does not exist" && exit 1 + +echo "> Test successful" \ No newline at end of file diff --git a/src/lofreq/call/test_data/script.sh b/src/lofreq/call/test_data/script.sh new file mode 100644 index 00000000..9a90bf48 --- /dev/null +++ b/src/lofreq/call/test_data/script.sh @@ -0,0 +1,10 @@ +# pear test data + +# Test data was obtained from https://github.com/snakemake/snakemake-wrappers/tree/master/bio/lofreq/call/test/data + +if [ ! -d /tmp/snakemake-wrappers ]; then + git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers +fi + +cp -r /tmp/snakemake-wrappers/bio/lofreq/call/test/data/* src/lofreq/call/test_data +