expressions in iwdr

Author: JensKrumsieck

CHANGELOG.md

@@ -2,12 +2,12 @@
 ## 🚀 Features
 - added NetworkAccess Requirment via `--net/--enable-network` in `s4n tool create` #104
 - Support InlineTools in Workflow step #111
-- Support Files and Directories as `InitialWorkDirRequirement` (in additon to Dirents)
+- Support Expressions, Files and Directories as `InitialWorkDirRequirement` (in additon to Dirents)
 
 ## 🐛 Bugfixes
 - fixed a bug with Dockerfile path resolution
 - handle NetworkAccess Requirment in runner
-- ramping up runner conformance from 160/378 to 177/378
+- ramping up runner conformance from 160/378 to 179/378
 
 # v0.5.2
 ## 🐛 Bugfixes

crates/cwl-execution/src/validate.rs

@@ -125,6 +125,15 @@ fn set_placeholder_values_requirements(requirements: &mut Vec<Requirement>, runt
                             Entry::Include(include.clone())
                         }
                     }
+                } else if let WorkDirItem::Expression(expr) = listing {
+                    // this kind of expression seems to be unfolding into File or Directory itself.
+                    // So we just need to find the correct input and set it to listing
+                    let re = Regex::new(r"\$\(inputs.([\w.]*)\)").unwrap();
+                    if let Ok(Some(caps)) = re.captures(expr) {
+                        if let Some(input) = runtime.inputs.get(&caps[1]) {
+                            *listing = WorkDirItem::FileOrDirectory(Box::new(input.clone()));
+                        }
+                    }
                 }
             }
         }

crates/cwl/src/requirements.rs

@@ -133,8 +133,8 @@ fn get_entry_name(input: &str) -> String {
 #[serde(untagged)]
 pub enum WorkDirItem {
     Dirent(Dirent),
-    FileOrDirectory(Box<DefaultValue>),
     Expression(String),
+    FileOrDirectory(Box<DefaultValue>),
 }
 
 #[derive(Serialize, Deserialize, Debug, PartialEq, Clone)]