From ba7eaf21f6d8e3af51f81ad29ec3e1ef66403dea Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@seqera.io>
Date: Fri, 23 Feb 2024 09:42:47 +0100
Subject: [PATCH] 10 minute hack to try to parse proper input structure from
 module processes, for meta.yml

---
 nf_core/components/nfcore_component.py | 30 ++++++++++++++++++--------
 nf_core/modules/lint/meta_yml.py       |  2 ++
 2 files changed, 23 insertions(+), 9 deletions(-)

diff --git a/nf_core/components/nfcore_component.py b/nf_core/components/nfcore_component.py
index 2f73afe9d3..f8c277a7a4 100644
--- a/nf_core/components/nfcore_component.py
+++ b/nf_core/components/nfcore_component.py
@@ -166,15 +166,27 @@ def get_inputs_from_main_nf(self):
             log.info(f"Could not find any inputs in {self.main_nf}")
             return inputs
         input_data = data.split("input:")[1].split("output:")[0]
-        regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))"
-        matches = re.finditer(regex, input_data, re.MULTILINE)
-        for _, match in enumerate(matches, start=1):
-            if match.group(3):
-                input_val = match.group(3).split(",")[0]  # handle `files, stageAs: "inputs/*"` cases
-                inputs.append(input_val)
-            elif match.group(4):
-                input_val = match.group(4).split(",")[0]  # handle `files, stageAs: "inputs/*"` cases
-                inputs.append(input_val)
+        for line in input_data.split("\n"):
+            theseinputs = []
+            regex = r"(val|path)\s*(\(([^)]+)\)|\s*([^)\s,]+))"
+            matches = re.finditer(regex, line)
+            for _, match in enumerate(matches, start=1):
+                input_type = None
+                input_val = None
+                if match.group(1):
+                    input_type = match.group(1)
+                if match.group(3):
+                    input_val = match.group(3).split(",")[0]  # handle `files, stageAs: "inputs/*"` cases
+                elif match.group(4):
+                    input_val = match.group(4).split(",")[0]  # handle `files, stageAs: "inputs/*"` cases
+                if input_type and input_val:
+                    theseinputs.append({
+                        input_val: {
+                            "type": input_type
+                        }
+                    })
+            if len(theseinputs) > 0:
+                inputs.append(theseinputs)
         log.info(f"Found {len(inputs)} inputs in {self.main_nf}")
         self.inputs = inputs
 
diff --git a/nf_core/modules/lint/meta_yml.py b/nf_core/modules/lint/meta_yml.py
index 481d50b3ef..6718ed5c21 100644
--- a/nf_core/modules/lint/meta_yml.py
+++ b/nf_core/modules/lint/meta_yml.py
@@ -40,6 +40,8 @@ def meta_yml(module_lint_object: ComponentLint, module: NFCoreComponent) -> None
     """
 
     module.get_inputs_from_main_nf()
+    print(yaml.dump({"input": module.inputs}))
+    exit()
     module.get_outputs_from_main_nf()
     # Check if we have a patch file, get original file in that case
     meta_yaml = None