From aefe580cd86ae2507ad6fb251ce406f03bbe8b4f Mon Sep 17 00:00:00 2001 From: emmarousseau Date: Wed, 27 Mar 2024 14:03:52 +0100 Subject: [PATCH] Fix file names and make output a required argument --- src/samtools/flagstat/config.vsh.yaml | 1 + src/samtools/flagstat/test.sh | 4 ++-- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/src/samtools/flagstat/config.vsh.yaml b/src/samtools/flagstat/config.vsh.yaml index c3374a37..9a33a3e3 100644 --- a/src/samtools/flagstat/config.vsh.yaml +++ b/src/samtools/flagstat/config.vsh.yaml @@ -28,6 +28,7 @@ argument_groups: description: | File containing samtools stats output. direction: output + required: true example: output.flagstat resources: diff --git a/src/samtools/flagstat/test.sh b/src/samtools/flagstat/test.sh index 43a52578..fc81e47a 100644 --- a/src/samtools/flagstat/test.sh +++ b/src/samtools/flagstat/test.sh @@ -15,7 +15,7 @@ echo ">>> Checking whether output is non-empty" echo ">>> Checking whether output is correct" diff "$meta_resources_dir/test_data/a.flagstat" "$meta_resources_dir/test_data/a_ref.flagstat" || \ - (echo "Output file chr19.flagstat does not match expected output" && exit 1) + (echo "Output file ca.flagstat does not match expected output" && exit 1) rm "$meta_resources_dir/test_data/a.flagstat" @@ -36,7 +36,7 @@ echo ">>> Checking whether output is non-empty" echo ">>> Checking whether output is correct" diff "$meta_resources_dir/test_data/test.paired_end.sorted.flagstat" "$meta_resources_dir/test_data/test_ref.paired_end.sorted.flagstat" || \ - (echo "Output file chr19.flagstat does not match expected output" && exit 1) + (echo "Output file test.pared_end.sorted.flagstat does not match expected output" && exit 1) rm "$meta_resources_dir/test_data/test.paired_end.sorted.flagstat"