diff --git a/src/bedtools/bedtools_bamtobed/config.vsh.yaml b/src/bedtools/bedtools_bamtobed/config.vsh.yaml index 85c0ff86..dc23da6d 100644 --- a/src/bedtools/bedtools_bamtobed/config.vsh.yaml +++ b/src/bedtools/bedtools_bamtobed/config.vsh.yaml @@ -27,6 +27,7 @@ argument_groups: arguments: - name: --output alternatives: -o + required: true type: file direction: output description: Output BED file. diff --git a/src/bedtools/bedtools_bamtobed/test.sh b/src/bedtools/bedtools_bamtobed/test.sh index 6e456c14..6a47d240 100644 --- a/src/bedtools/bedtools_bamtobed/test.sh +++ b/src/bedtools/bedtools_bamtobed/test.sh @@ -1,7 +1,7 @@ #!/bin/bash # exit on error -set -e +set -eo pipefail # directory of the bam file test_data="$meta_resources_dir/test_data"