From 7846fe69c32532a8759219781005f62c670a950e Mon Sep 17 00:00:00 2001
From: emmarousseau <emmarou1@icloud.com>
Date: Fri, 22 Mar 2024 11:14:47 +0100
Subject: [PATCH] first basic test working & changed source container for a
 more recent version

---
 src/samtools/flagstat/config.vsh.yaml | 2 +-
 src/samtools/flagstat/script.sh       | 6 ++++--
 src/samtools/flagstat/test.sh         | 6 +++---
 3 files changed, 8 insertions(+), 6 deletions(-)

diff --git a/src/samtools/flagstat/config.vsh.yaml b/src/samtools/flagstat/config.vsh.yaml
index bf80f418..b1a81d4d 100644
--- a/src/samtools/flagstat/config.vsh.yaml
+++ b/src/samtools/flagstat/config.vsh.yaml
@@ -40,7 +40,7 @@ test_resources:
     path: test_data
 engines:
   - type: docker
-    image: quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1
+    image: quay.io/biocontainers/samtools:1.3.1--h9071d68_10
     setup:
       - type: docker
         run: |
diff --git a/src/samtools/flagstat/script.sh b/src/samtools/flagstat/script.sh
index 16263079..1d7c8e11 100644
--- a/src/samtools/flagstat/script.sh
+++ b/src/samtools/flagstat/script.sh
@@ -5,7 +5,9 @@
 
 set -e
 
+output_file="$par_output"
+
 samtools flagstat \
-    "$par_input_bam" \
-    > "$par_output_stats"
+    "$par_bam" \
+    > "$output_file"
     
\ No newline at end of file
diff --git a/src/samtools/flagstat/test.sh b/src/samtools/flagstat/test.sh
index 80fda0f5..1da36e2b 100644
--- a/src/samtools/flagstat/test.sh
+++ b/src/samtools/flagstat/test.sh
@@ -8,14 +8,14 @@ echo ">>> Testing $meta_functionality_name"
   --output "$meta_resources_dir/test_data/chr19.flagstat"
 
 echo ">>> Checking whether output exists"
-[ ! -f "test_data/chr19.flagstat" ] && echo "File 'chr19.flagstat' does not exist!" && exit 1
+[ ! -f "$meta_resources_dir/test_data/chr19.flagstat" ] && echo "File 'chr19.flagstat' does not exist!" && exit 1
 
 echo ">>> Checking whether output is non-empty"
-[ ! -s "test_data/chr19.flagstat" ] && echo "File 'chr19.flagstat' is empty!" && exit 1
+[ ! -s "$meta_resources_dir/test_data/chr19.flagstat" ] && echo "File 'chr19.flagstat' is empty!" && exit 1
 
 echo ">>> Checking whether output is correct"
 diff "$meta_resources_dir/test_data/chr19.flagstat" "$meta_resources_dir/test_data/chr19_ref.flagstat" || \
-    (echo "Output does not match expected output." && exit 1)
+    (echo "Output file chr19.flagstat does not match expected output" && exit 1)
 
 rm "$meta_resources_dir/test_data/chr19.flagstat"