Merge pull request #418 from microbiomedata/417-could-not-process-output-file-not-found-opaver_web_pathjson

mflynn-lanl · web-flow · commit 87e9a588690a · 2025-09-18T10:52:16.000-06:00
fix the optional opaver_web_path_json file
diff --git a/data/workflow/WDL/metaG/annotation_output.wdl b/data/workflow/WDL/metaG/annotation_output.wdl
@@ -29,8 +29,8 @@ workflow annotation_output {
         container = container
     }
     output{
-        File protein_size_hist = annotation_vis.opaver_web_path_json 
-        File opaver_web_path_json = annotation_vis.protein_size_hist
+        File protein_size_hist = annotation_vis.protein_size_hist
+        File? opaver_web_path_json = annotation_vis.opaver_web_path_json 
     }
 }
 
@@ -80,7 +80,7 @@ task annotation_vis{
 
     output {
         File protein_size_hist = "~{OUTPATH}/~{projectName}.protein_size_histogram.html"
-        File opaver_web_path_json = "~{OUTPATH}/opaver_web_path.json"
+        File? opaver_web_path_json = "~{OUTPATH}/opaver_web_path.json"
     }
 
     runtime {

Original file line number	Diff line number	Diff line change
`@@ -29,8 +29,8 @@ workflow annotation_output {`
`29`	`29`	`container = container`
`30`	`30`	`}`
`31`	`31`	`output{`
`32`		`- File protein_size_hist = annotation_vis.opaver_web_path_json`
`33`		`- File opaver_web_path_json = annotation_vis.protein_size_hist`
	`32`	`+ File protein_size_hist = annotation_vis.protein_size_hist`
	`33`	`+ File? opaver_web_path_json = annotation_vis.opaver_web_path_json`
`34`	`34`	`}`
`35`	`35`	`}`
`36`	`36`
`@@ -80,7 +80,7 @@ task annotation_vis{`
`80`	`80`
`81`	`81`	`output {`
`82`	`82`	`File protein_size_hist = "~{OUTPATH}/~{projectName}.protein_size_histogram.html"`
`83`		`- File opaver_web_path_json = "~{OUTPATH}/opaver_web_path.json"`
	`83`	`+ File? opaver_web_path_json = "~{OUTPATH}/opaver_web_path.json"`
`84`	`84`	`}`
`85`	`85`
`86`	`86`	`runtime {`