From c1043613a0d58195c78044cc8fa05cbbfe0a8a81 Mon Sep 17 00:00:00 2001
From: Hendrik Cannoodt <hendrik.cannoodt@gmail.com>
Date: Fri, 26 Jan 2024 10:48:50 +0100
Subject: [PATCH] improve implementation of regular script and test script

---
 src/bgzip/config.vsh.yaml              | 48 +++++++++++++++++++-------
 src/bgzip/test_data/README.md          | 13 +++++++
 src/bgzip/{test => test_data}/test.vcf |  0
 3 files changed, 48 insertions(+), 13 deletions(-)
 create mode 100644 src/bgzip/test_data/README.md
 rename src/bgzip/{test => test_data}/test.vcf (100%)

diff --git a/src/bgzip/config.vsh.yaml b/src/bgzip/config.vsh.yaml
index a4fe18e3..bae1eb20 100644
--- a/src/bgzip/config.vsh.yaml
+++ b/src/bgzip/config.vsh.yaml
@@ -20,26 +20,48 @@ functionality:
       direction: output
       description: compressed or decompressed output
       required: true
-    - name: --extra
-      type: string
-      description: extra arguments to pass to bgzip
-      required: false
-    - name: --threads
-      type: integer
-      description: number of threads to use
-      required: false
-      default: 1
+    - name: --decompress
+      alternatives: -d
+      type: boolean_true
+      description: decompress the input file
   resources:
     - type: bash_script
       text: |
-        bgzip -c "$par_extra" --threads "$par_threads" "$par_input" > "$par_output"
+        [[ "$par_decompress" == "false" ]] && unset par_decompress
+        bgzip -c \
+          ${meta_cpus:+--threads "${meta_cpus}"} \
+          ${par_decompress:+-d} \
+          "$par_input" > "$par_output"
   test_resources:
     - type: bash_script
       text: |
-        "$meta_executable" --input "$meta_resources_dir/test/test.vcf" --output "$meta_resources_dir/test.vcf.gz"
+        set -e
+
+        "$meta_executable" --input "$meta_resources_dir/test_data/test.vcf" --output "test.vcf.gz"
+
+        echo ">> Checking output of compressing"
+        [ ! -f "test.vcf.gz" ] && echo "Output file test.vcf.gz does not exist" && exit 1
+
+        "$meta_executable" --input "test.vcf.gz" --output "test.vcf" --decompress
+
+        echo ">> Checking output of decompressing"
+        [ ! -f "test.vcf" ] && echo "Output file test.vcf does not exist" && exit 1
+
+        echo ">> Checking original and decompressed files are the same"
+        set +e
+        cmp --silent -- "$meta_resources_dir/test_data/test.vcf" "test.vcf"
+        [ $? -ne 0 ] && echo "files are different" && exit 1
+        set -e
+        
+        echo "> Test successful"
     - type: file
-      path: test
+      path: test_data
 
 platforms:
   - type: docker
-    image: quay.io/biocontainers/htslib:1.19--h81da01d_0
\ No newline at end of file
+    image: quay.io/biocontainers/htslib:1.19--h81da01d_0
+    setup:
+      - type: docker
+        run: |
+          bgzip -h | grep 'Version:' 2>&1 |  sed 's/Version:\s\(.*\)/arriba: "\1"/' > /var/software_versions.txt
+  - type: nextflow
\ No newline at end of file
diff --git a/src/bgzip/test_data/README.md b/src/bgzip/test_data/README.md
new file mode 100644
index 00000000..ce46295a
--- /dev/null
+++ b/src/bgzip/test_data/README.md
@@ -0,0 +1,13 @@
+# arriba test data
+
+Test data was obtained from https://github.com/snakemake/snakemake-wrappers/tree/master/bio/bgzip/test.
+
+__author__ = "William Rowell"
+__copyright__ = "Copyright 2020, William Rowell"
+__email__ = "wrowell@pacb.com"
+__license__ = "MIT"
+
+```bash
+git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers
+cp -r /tmp/snakemake-wrappers/bio/bgzip/test/* src/bgzip/test_data
+```
\ No newline at end of file
diff --git a/src/bgzip/test/test.vcf b/src/bgzip/test_data/test.vcf
similarity index 100%
rename from src/bgzip/test/test.vcf
rename to src/bgzip/test_data/test.vcf