Make dppp step optional, depending on whether the data was already compressed

compress_pipeline.cwl

@@ -23,7 +23,7 @@ outputs:
   outputSource:
   - inspect_step/inspect_file
 - id: logfile
-  type: File[]
+  type: File[]?
   outputSource:
   - dppp/logfile
 - id: compressed
@@ -45,6 +45,9 @@ outputs:
 - id: keep_input
   type: boolean
   outputSource: identify_issues/skip_compress
+- id: input_storage_manager
+  type: string
+  outputSource: identify_issues/input_storage_manager
 
 steps:
 - id: identify_issues
@@ -60,6 +63,7 @@ steps:
   - unfixable_issues
   - msout
   - skip_compress
+  - input_storage_manager
 - id: fix_ai_2013
   in:
   - id: msin
@@ -106,7 +110,10 @@ steps:
 - id: extract_sip_meta
   in:
   - id: msin
-    source: dppp/msout
+    source: 
+    - dppp/msout
+    - msin
+    pickValue: first_non_null
   - id: compressed_file
     source: compress/compressed
   - id: skip
@@ -131,6 +138,9 @@ steps:
     default: Dysco
   - id: databitrate
     default: 10
+  - id: input_storage_manager
+    source: identify_issues/input_storage_manager
+  when: $(inputs.input_storage_manager != "DyscoStorageManager")
   run: steps/DPPP.cwl
   out:
   - id: msout
@@ -164,7 +174,10 @@ steps:
   label: compress
   in:
   - id: directory
-    source: dppp/msout
+    source: 
+    - dppp/msout
+    - msin
+    pickValue: first_non_null
   - id: skip
     source: identify_issues/skip_compress
   when: $(inputs.skip == false)
@@ -174,9 +187,15 @@ steps:
 - id: inspect_step
   in:
   - id: msin
-    source: dppp/msout
+    source: 
+    - dppp/msout
+    - msin
+    pickValue: first_non_null
   - id: inspect_file_name
-    source: dppp/msout
+    source: 
+    - dppp/msout
+    - msin
+    pickValue: first_non_null
     valueFrom: $(self.basename + "_inspect.h5")
   run: steps/create_inspect_dataset.cwl
   out: