3 files changed, 28 insertions, 6 deletions
diff --git a/workflow/pandoc-filter-tool.cwl b/workflow/pandoc-filter-tool.cwl
index a433081..d657d08 100755
--- a/workflow/pandoc-filter-tool.cwl
+++ b/workflow/pandoc-filter-tool.cwl
@@ -13,20 +13,25 @@ inputs:
     type: File
     inputBinding:
       position: 1
+  output_format:
+    type: string
+    inputBinding:
+      prefix: -t
+      position: 2
 
 outputs:
   html_with_rdfa:
     type: File
     outputBinding:
-      glob: output
+      glob: output.${output_format}
   latex_with_xmp:
     type: File
     outputBinding:
-      glob: output
+      glob: output.${output_format}
   markdown:
     type: File
     outputBinding:
-      glob: output
+      glob: output.${output_format}
 stdout: output
 
 baseCommand: pandoc
diff --git a/workflow/phase1.cwl b/workflow/phase1.cwl
index f531e69..1aa0bc2 100755
--- a/workflow/phase1.cwl
+++ b/workflow/phase1.cwl
@@ -18,6 +18,8 @@ steps:
   strip:
     in:
       input_file: annotated_markdown
+      output_format:
+        default: commonmark
     run: pandoc-filter-tool.cwl
     out:
     - markdown
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