Add temp fix findstates

src/workflows/run_benchmark/main.nf

@@ -1,5 +1,5 @@
 workflow auto {
-  findStates(params, meta.config)
+  findStatesTemp(params, meta.config)
     | meta.workflow.run(
       auto: [publish: "state"]
     )
@@ -57,14 +57,14 @@ workflow run_wf {
 
       // use the 'filter' argument to only run a defined method or all methods
       filter: { id, state, comp ->
-        def method_check = !state.method_ids || state.method_ids.contains(comp.config.functionality.name)
+        def method_check = !state.method_ids || state.method_ids.contains(comp.config.name)
 
         method_check
       },
 
       // define a new 'id' by appending the method name to the dataset id
       id: { id, state, comp ->
-        id + "." + comp.config.functionality.name
+        id + "." + comp.config.name
       },
       // use 'fromState' to fetch the arguments the component requires from the overall state
       fromState: [
@@ -74,7 +74,7 @@ workflow run_wf {
       // use 'toState' to publish that component's outputs to the overall state
       toState: { id, output, state, comp ->
         state + [
-          method_id: comp.config.functionality.name,
+          method_id: comp.config.name,
           method_output: output.output
         ]
       }
@@ -84,7 +84,7 @@ workflow run_wf {
     | runEach(
       components: metrics,
       id: { id, state, comp ->
-        id + "." + comp.config.functionality.name
+        id + "." + comp.config.name
       },
       // use 'fromState' to fetch the arguments the component requires from the overall state
       fromState: [
@@ -94,7 +94,7 @@ workflow run_wf {
       // use 'toState' to publish that component's outputs to the overall state
       toState: { id, output, state, comp ->
         state + [
-          metric_id: comp.config.functionality.name,
+          metric_id: comp.config.name,
           metric_output: output.output
         ]
       }
@@ -181,4 +181,122 @@ workflow run_wf {
 
   emit:
   output_ch
+}
+
+
+// temp fix for rename_keys typo
+
+def findStatesTemp(Map params, Map config) {
+  def auto_config = deepClone(config)
+  def auto_params = deepClone(params)
+
+  auto_config = auto_config.clone()
+  // override arguments
+  auto_config.argument_groups = []
+  auto_config.arguments = [
+    [
+      type: "string",
+      name: "--id",
+      description: "A dummy identifier",
+      required: false
+    ],
+    [
+      type: "file",
+      name: "--input_states",
+      example: "/path/to/input/directory/**/state.yaml",
+      description: "Path to input directory containing the datasets to be integrated.",
+      required: true,
+      multiple: true,
+      multiple_sep: ";"
+    ],
+    [
+      type: "string",
+      name: "--filter",
+      example: "foo/.*/state.yaml",
+      description: "Regex to filter state files by path.",
+      required: false
+    ],
+    // to do: make this a yaml blob?
+    [
+      type: "string",
+      name: "--rename_keys",
+      example: ["newKey1:oldKey1", "newKey2:oldKey2"],
+      description: "Rename keys in the detected input files. This is useful if the input files do not match the set of input arguments of the workflow.",
+      required: false,
+      multiple: true,
+      multiple_sep: ";"
+    ],
+    [
+      type: "string",
+      name: "--settings",
+      example: '{"output_dataset": "dataset.h5ad", "k": 10}',
+      description: "Global arguments as a JSON glob to be passed to all components.",
+      required: false
+    ]
+  ]
+  if (!(auto_params.containsKey("id"))) {
+    auto_params["id"] = "auto"
+  }
+
+  // run auto config through processConfig once more
+  auto_config = processConfig(auto_config)
+
+  workflow findStatesTempWf {
+    helpMessage(auto_config)
+
+    output_ch = 
+      channelFromParams(auto_params, auto_config)
+        | flatMap { autoId, args ->
+
+          def globalSettings = args.settings ? readYamlBlob(args.settings) : [:]
+
+          // look for state files in input dir
+          def stateFiles = args.input_states
+
+          // filter state files by regex
+          if (args.filter) {
+            stateFiles = stateFiles.findAll{ stateFile ->
+              def stateFileStr = stateFile.toString()
+              def matcher = stateFileStr =~ args.filter
+              matcher.matches()}
+          }
+
+          // read in states
+          def states = stateFiles.collect { stateFile ->
+            def state_ = readTaggedYaml(stateFile)
+            [state_.id, state_]
+          }
+
+          // construct renameMap
+          if (args.rename_keys) {
+            def renameMap = args.rename_keys.collectEntries{renameString ->
+              def split = renameString.split(":")
+              assert split.size() == 2: "Argument 'rename_keys' should be of the form 'newKey:oldKey,newKey:oldKey'"
+              split
+            }
+
+            // rename keys in state, only let states through which have all keys
+            // also add global settings
+            states = states.collectMany{id, state ->
+              def newState = [:]
+
+              for (key in renameMap.keySet()) {
+                def origKey = renameMap[key]
+                if (!(state.containsKey(origKey))) {
+                  return []
+                }
+                newState[key] = state[origKey]
+              }
+
+              [[id, globalSettings + newState]]
+            }
+          }
+
+          states
+        }
+    emit:
+    output_ch
+  }
+
+  return findStatesTempWf
 }