Make calls of jar files and wrappers more robust

cbg-ethz · Apr 13, 2020 · 9a1c6fc · 9a1c6fc
1 parent 9925a5f
commit 9a1c6fc
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Showing 2 changed files with 11 additions and 11 deletions.
diff --git a/functions.sh b/functions.sh
@@ -28,18 +28,18 @@ bam2sam() {
 }
 
 indelFixer() {
-    if [[ -z "${CONDA_PREFIX:-}" ]]; then
-        java -XX:+UseParallelGC -XX:NewRatio=9 -Xms2G -Xmx10G -jar $@
-    else
+    if [[ -x "$(command -v $1)" ]]; then
         $1 -XX:+UseParallelGC -XX:NewRatio=9 -Xms2G -Xmx10G ${@:2}
+    else
+        java -XX:+UseParallelGC -XX:NewRatio=9 -Xms2G -Xmx10G -jar $@
     fi
 }
 
 consensusFixer() {
-    if [[ -z "${CONDA_PREFIX:-}" ]]; then
-	    java -XX:+UseParallelGC -XX:NewRatio=9 -Xms2G -Xmx10G -jar $@
-    else
+    if [[ -x "$(command -v $1)" ]]; then
         $1 -XX:+UseParallelGC -XX:NewRatio=9 -Xms2G -Xmx10G ${@:2}
+    else
+	    java -XX:+UseParallelGC -XX:NewRatio=9 -Xms2G -Xmx10G -jar $@
     fi
 }
 
@@ -48,9 +48,9 @@ QuasiRecomb() {
 }
 
 SamToFastq() {
-    if [[ -z "${CONDA_PREFIX:-}" ]]; then
-        java -jar $1 SamToFastq ${@:2}
-    else
+    if [[ -x "$(command -v $1)" ]]; then
         $1 SamToFastq ${@:2}
+    else
+        java -jar $1 SamToFastq ${@:2}
     fi
 }
diff --git a/rules/common.smk b/rules/common.smk
@@ -51,8 +51,8 @@ class VpipeConfig(object):
             'prinseq': __RECORD__(value="prinseq-lite.pl", type=str),
             'fastqc': __RECORD__(value="fastqc", type=str),
             'vicuna': __RECORD__(value="vicuna", type=str),
-            'indelfixer': __RECORD__(value="IndelFixer.jar", type=str),
-            'consensusfixer': __RECORD__(value="ConsensusFixer.jar", type=str),
+            'indelfixer': __RECORD__(value="InDelFixer", type=str),
+            'consensusfixer': __RECORD__(value="ConsensusFixer", type=str),
             'picard': __RECORD__(value="picard", type=str),
             'bwa': __RECORD__(value="bwa", type=str),
             'bowtie_idx': __RECORD__(value="bowtie2-build", type=str),