add argument output_format to workflow

1 files changed, 18 insertions, 3 deletions

diff --git a/workflow/phases.cwl b/workflow/phases.cwl
index 95df658..e4562be 100755
--- a/workflow/phases.cwl
+++ b/workflow/phases.cwl
@@ -12,10 +12,10 @@ inputs:
 outputs:
   annotated_html:
     type: File
-    outputSource: convert/html_with_rdfa
+    outputSource: convert_to_html/html_with_rdfa
   annotated_pdf:
     type: File
-    outputSource: convert/latex_with_xmp
+    outputSource: convert_to_pdf/latex_with_xmp
   markdown_with_metadata:
     type: File
     outputSource: extract/markdown
@@ -24,9 +24,20 @@ outputs:
     outputSource: strip/markdown
 
 steps:
-  convert:
+  convert_to_html:
     in:
       input_file: annotated_markdown
+      output_format:
+        default: html
+    run: pandoc-filter-tool.cwl
+    out:
+    - html_with_rdfa
+    - latex_with_xmp
+  convert_to_pdf:
+    in:
+      input_file: annotated_markdown
+      output_format:
+        default: pdf
     run: pandoc-filter-tool.cwl
     out:
     - html_with_rdfa
@@ -34,12 +45,16 @@ steps:
   extract:
     in:
       input_file: annotated_markdown
+      output_format:
+        default: commonmark
     run: pandoc-filter-tool.cwl
     out:
     - markdown
   strip:
     in:
       input_file: annotated_markdown
+      output_format:
+        default: commonmark
     run: pandoc-filter-tool.cwl
     out:
     - markdown