From 2c38cd8f39f7cfe7fc287b7199fd7cc44d665a1e Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Wed, 19 Mar 2025 14:00:35 +0100
Subject: [PATCH] small update to DSL1 to DSL2 conversion
---
src/process.py | 39 +++++++++++++++++++++++----------------
1 file changed, 23 insertions(+), 16 deletions(-)
diff --git a/src/process.py b/src/process.py
index d81cd61..c791e70 100644
--- a/src/process.py
+++ b/src/process.py
@@ -261,6 +261,7 @@ class Process(Nextflow_Building_Blocks):
for line in code.split("\n"):
+ placed = False
#Case there is a single channel as an input -> doesn't use from to import channel -> uses file (see https://github.com/nextflow-io/nextflow/blob/45ceadbdba90b0b7a42a542a9fc241fb04e3719d/docs/process.rst)
patterns = [constant.FILE, constant.PATH]
@@ -271,25 +272,30 @@ class Process(Nextflow_Building_Blocks):
extracted = match.group(1).strip()
except:
extracted = match.group(2).strip()
-
+ placed = True
add_channel(extracted)
self.raw_input_names.append(extracted)
-
- #Case there are multiple channels as input (e.g. channel1.mix(channel2))
- pattern = constant.FROM
- for match in re.finditer(pattern, line+"\n"):
- extracted = match.group(1).strip()
- self.raw_input_names.append(extracted)
-
- if(bool(re.fullmatch(constant.WORD, extracted))):
- add_channel(extracted)
- else:
- from .operation import Operation
- operation = Operation(code=extracted, origin=self.origin)
- operation.initialise()
- operation.is_defined_in_process(self)
- self.inputs+=operation.get_origins()
+ if(not placed):
+ #Case there are multiple channels as input (e.g. channel1.mix(channel2))
+ pattern = constant.FROM
+ for match in re.finditer(pattern, line+"\n"):
+ extracted = match.group(1).strip()
+ self.raw_input_names.append(extracted)
+ placed = True
+ if(bool(re.fullmatch(constant.WORD, extracted))):
+ add_channel(extracted)
+ else:
+ from .operation import Operation
+ operation = Operation(code=extracted, origin=self.origin)
+ operation.initialise()
+ operation.is_defined_in_process(self)
+ self.inputs+=operation.get_origins()
+
+ if(not placed):
+ if(re.fullmatch(constant.WORD, line.strip())):
+ add_channel(line)
+ self.raw_input_names.append(line)
#self.inputs = list(set(self.inputs))#TODO Check this
@@ -453,6 +459,7 @@ class Process(Nextflow_Building_Blocks):
for line in code.split("\n"):
temp = process_2_DSL2(line.split(" from ")[0])
lines.append(temp)
+ #TODO -> need to determine if it's on it's own is it either a path or val
code = "\n".join(lines)
return code
--
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