Merge remote-tracking branch 'origin/develop_0_9' into port_integers_as_doubles

Author: rcannood

docs/paper/paper.md

@@ -2,29 +2,37 @@
 title: 'Viash: A meta-framework for building reusable workflow modules'
 bibliography: library.bib
 authors:
-- name: Robrecht Cannoodt
+- given-names: Robrecht
+  surname: Cannoodt
   email: robrecht@data-intuitive.com
   orcid: 0000-0003-3641-729X
   corresponding: yes
   affiliation: 1, 2, 3
-- name: Hendrik Cannoodt
+- given-names: Hendrik
+  surname: Cannoodt
   orcid: 0000-0002-0032-6719
   affiliation: '1'
-- name: Dries Schaumont
+- given-names: Dries
+  surname: Schaumont
   orcid: 0000-0002-4389-0440
   affiliation: '1'
-- name: Kai Waldrant
+- given-names: Kai
+  surname: Waldrant
   orcid: 0009-0003-8555-1361
   affiliation: '1'
-- name: Eric Van de Kerckhove
+- given-names: Eric
+  surname: Van de Kerckhove
   affiliation: '1'
-- name: Andy Boschmans
+- given-names: Andy
+  surname: Boschmans
   orcid: 0009-0008-8793-4661
   affiliation: '1'
-- name: Dries De Maeyer
+- given-names: Dries
+  surname: De Maeyer
   orcid: 0000-0002-1314-3348
   affiliation: '4'
-- name: Toni Verbeiren
+- given-names: Toni
+  surname: Verbeiren
   email: toni@data-intuitive.com
   orcid: 0000-0002-7007-6866
   corresponding: yes

src/main/scala/io/viash/runners/nextflow/NextflowHelper.scala

@@ -73,12 +73,12 @@ object NextflowHelper {
       .replace("'''", "\\'\\'\\'")
 
     // IMPORTANT! difference between code below and BashWrapper:
-    // script is stored as `.viash_script.sh`.
+    // script is stored as `.viash_script.${ext}`.
     val scriptPath = "$tempscript"
 
     val executionCode = 
       s"""set -e
-        |tempscript=".viash_script.sh"
+        |tempscript=".viash_script.${res.companion.extension}"
         |cat > "$scriptPath" << VIASHMAIN
         |$escapedCode
         |VIASHMAIN