POSIX-compatible command testing

bio-miga · May 21, 2024 · 44c0930 · 44c0930
1 parent cbaae60
commit 44c0930
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Showing 3 changed files with 3 additions and 3 deletions.
diff --git a/lib/miga/version.rb b/lib/miga/version.rb
@@ -12,7 +12,7 @@ module MiGA
   # - String indicating release status:
   #   - rc* release candidate, not released as gem
   #   - [0-9]+ stable release, released as gem
-  VERSION = [1.3, 15, 2].freeze
+  VERSION = [1.3, 15, 3].freeze
 
   ##
   # Nickname for the current major.minor version.

diff --git a/scripts/miga.bash b/scripts/miga.bash
@@ -16,7 +16,7 @@ function exists { [[ -e "$1" ]] ; }
 function fx_exists { [[ $(type -t "$1") == "function" ]] ; }
 
 # Override gzip with pigz (if available)
-if which -s pigz ; then
+if command -v pigz &>/dev/null ; then
   function gzip { pigz -p ${CORES:-2} "$@" ; }
 fi
 

diff --git a/scripts/trimmed_reads.bash b/scripts/trimmed_reads.bash
@@ -31,7 +31,7 @@ FastQ.tag.rb -i "$in1" -p "$b-" -s "/1" -o "$b.1.fastq.gz"
 
 # Multitrim
 CMD="multitrim.py --level 9 --threads $CORES -o $b"
-which -s pigz && CMD="$CMD --zip pigz"
+command -v pigz &>/dev/null && CMD="$CMD --zip pigz"
 if [[ -s "$b.2.fastq.gz" ]] ; then
   # Paired
   $CMD -1 "$b.1.fastq.gz" -2 "$b.2.fastq.gz"