clean up helper functions

src/bd_rhapsody/bd_rhapsody_make_reference/test.sh

@@ -11,21 +11,18 @@ assert_file_doesnt_exist() {
   [ ! -f "$1" ] || { echo "File '$1' exists but shouldn't" && exit 1; }
 }
 assert_file_empty() {
-  #  () will execute in a shubshell, could you use {;}?
   [ ! -s "$1" ] || { echo "File '$1' is not empty but should be" && exit 1; }
 }
 assert_file_not_empty() {
-  # [ -s "$1" ] || (echo "File '$1' is empty but shouldn't be" && exit 1)
   [ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; }
 }
 assert_file_contains() {
-  # grep -q "$2" "$1" || (echo "File '$1' does not contain '$2'" && exit 1)
   grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
 }
 assert_file_not_contains() {
-  # grep -q "$2" "$1" && (echo "File '$1' contains '$2' but shouldn't" && exit 1)
   grep -q "$2" "$1" && { echo "File '$1' contains '$2' but shouldn't" && exit 1; }
 }
+#############################################
 
 in_fa="$meta_resources_dir/test_data/reference_small.fa"
 in_gtf="$meta_resources_dir/test_data/reference_small.gtf"

src/cutadapt/test.sh

@@ -6,25 +6,25 @@ set -eo pipefail
 #############################################
 # helper functions
 assert_file_exists() {
-  [ -f "$1" ] || (echo "File '$1' does not exist" && exit 1)
+  [ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; }
 }
 assert_file_doesnt_exist() {
-  [ ! -f "$1" ] || (echo "File '$1' exists but shouldn't" && exit 1)
+  [ ! -f "$1" ] || { echo "File '$1' exists but shouldn't" && exit 1; }
 }
 assert_file_empty() {
-  [ ! -s "$1" ] || (echo "File '$1' is not empty but should be" && exit 1)
+  [ ! -s "$1" ] || { echo "File '$1' is not empty but should be" && exit 1; }
 }
 assert_file_not_empty() {
-  [ -s "$1" ] || (echo "File '$1' is empty but shouldn't be" && exit 1)
+  [ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; }
 }
 assert_file_contains() {
-  grep -q "$2" "$1" || (echo "File '$1' does not contain '$2'" && exit 1)
+  grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
 }
 assert_file_not_contains() {
-  grep -q "$2" "$1" && (echo "File '$1' contains '$2' but shouldn't" && exit 1)
+  grep -q "$2" "$1" && { echo "File '$1' contains '$2' but shouldn't" && exit 1; }
 }
-
 #############################################
+
 mkdir test_multiple_output
 cd test_multiple_output
 

src/star/star_align_reads/test.sh

@@ -7,35 +7,34 @@ meta_executable="target/docker/star/star_align_reads/star_align_reads"
 meta_resources_dir="src/star/star_align_reads"
 ## VIASH END
 
-#########################################################################################
-
+#############################################
 # helper functions
 assert_file_exists() {
-  [ -f "$1" ] || (echo "File '$1' does not exist" && exit 1)
+  [ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; }
 }
 assert_file_doesnt_exist() {
-  [ ! -f "$1" ] || (echo "File '$1' exists but shouldn't" && exit 1)
+  [ ! -f "$1" ] || { echo "File '$1' exists but shouldn't" && exit 1; }
 }
 assert_file_empty() {
-  [ ! -s "$1" ] || (echo "File '$1' is not empty but should be" && exit 1)
+  [ ! -s "$1" ] || { echo "File '$1' is not empty but should be" && exit 1; }
 }
 assert_file_not_empty() {
-  [ -s "$1" ] || (echo "File '$1' is empty but shouldn't be" && exit 1)
+  [ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; }
 }
 assert_file_contains() {
-  grep -q "$2" "$1" || (echo "File '$1' does not contain '$2'" && exit 1)
+  grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
 }
 assert_file_not_contains() {
-  grep -q "$2" "$1" && (echo "File '$1' contains '$2' but shouldn't" && exit 1)
+  grep -q "$2" "$1" && { echo "File '$1' contains '$2' but shouldn't" && exit 1; }
 }
 assert_file_contains_regex() {
-  grep -q -E "$2" "$1" || (echo "File '$1' does not contain '$2'" && exit 1)
+  grep -q -E "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
 }
 assert_file_not_contains_regex() {
-  grep -q -E "$2" "$1" && (echo "File '$1' contains '$2' but shouldn't" && exit 1)
+  grep -q -E "$2" "$1" && { echo "File '$1' contains '$2' but shouldn't" && exit 1; }
 }
+#############################################
 
-#########################################################################################
 echo "> Prepare test data"
 
 cat > reads_R1.fastq <<'EOF'