biom-convert wrapper

EBI-Metagenomics · Mar 11, 2020 · 92d91b3 · 92d91b3
1 parent 56650be
commit 92d91b3
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Showing 2 changed files with 8 additions and 2 deletions.
diff --git a/tools/RNA_prediction/biom-convert/biom-convert.cwl b/tools/RNA_prediction/biom-convert/biom-convert.cwl
@@ -20,6 +20,7 @@ hints:
 #        version: [ "2.1.6" ]
 #
 
+baseCommand: [ "biom-convert.sh" ]
 
 inputs:
   biom:
@@ -62,8 +63,6 @@ inputs:
     inputBinding:
       prefix: --header-key
 
-baseCommand: [ "biom", "convert" ]
-
 arguments:
   - valueFrom: |
      ${ var ext = "";

diff --git a/tools/RNA_prediction/biom-convert/biom-convert.sh b/tools/RNA_prediction/biom-convert/biom-convert.sh
@@ -0,0 +1,7 @@
+#!/bin/bash
+
+# Biom convert wrapper - because Toil doesn't set the locale variables LC_ALL and LANG
+export LC_ALL="en_US.UTF-8"
+export LANG="en_US.UTF-8"
+
+biom convert "$@"