Don't compress sun targets

compress_pipeline.cwl

@@ -27,11 +27,11 @@ outputs:
   outputSource:
   - dppp/logfile
 - id: compressed
-  type: File
+  type: File?
   outputSource:
   - compress/compressed
 - id: ingest
-  type: Any
+  type: Any?
   outputSource:
   - format_ingest/ingest
 - id: applied_fixes
@@ -56,6 +56,7 @@ steps:
   - is_raw
   - unfixable_issues
   - msout
+  - skip_compress
 - id: fix_ai_2013
   in:
   - id: msin
@@ -105,6 +106,10 @@ steps:
     source: dppp/msout
   - id: compressed_file
     source: compress/compressed
+  - id: skip
+    valueFrom: $(self.includes("skip_compress"))
+    source: identify_issues/issue_list
+  when: $(inputs.skip == false)
   run: steps/extract_sip_meta.cwl
   out:
   - id: ingest
@@ -135,8 +140,12 @@ steps:
   - id: output_name
     default: compressed
   - id: file_name
-    valueFrom: $(self.basename)
+    valueFrom: $((self && self.basename) || "foo")
     source: compress/compressed
+  - id: skip
+    valueFrom: $(self.includes("skip_compress"))
+    source: identify_issues/issue_list
+  when: $(inputs.skip == false)
   run: steps/format_ingest.cwl
   out:
   - id: ingest
@@ -155,6 +164,10 @@ steps:
   in:
   - id: directory
     source: dppp/msout
+  - id: skip
+    valueFrom: $(self.includes("skip_compress"))
+    source: identify_issues/issue_list
+  when: $(inputs.skip == false)
   run: steps/compress.cwl
   out:
   - id: compressed

steps/identify_issues.cwl

@@ -42,6 +42,12 @@ outputs:
     glob: output.txt
     outputEval: $(JSON.parse(self[0].contents)['is_raw'])
     loadContents: true
+- id: skip_compress
+  type: boolean
+  outputBinding:
+    glob: output.txt
+    outputEval: $(JSON.parse(self[0].contents)['skip_compress'])
+    loadContents: true
 - id: msout
   type: Directory
   outputBinding: