From dde31389a0482406980cf2e6faa160e07b0782a8 Mon Sep 17 00:00:00 2001
From: George Marchment <georgemarchment@yahoo.fr>
Date: Tue, 18 Mar 2025 15:27:00 +0100
Subject: [PATCH] First workflow (EpiDiverse/snp) works A to Z by rewritting
and then running
---
src/nextflow_file.py | 20 ++++++++++++++++++++
src/workflow.py | 31 ++++++++++++++++++-------------
2 files changed, 38 insertions(+), 13 deletions(-)
diff --git a/src/nextflow_file.py b/src/nextflow_file.py
index ebdf62d..9329ac8 100644
--- a/src/nextflow_file.py
+++ b/src/nextflow_file.py
@@ -273,6 +273,26 @@ class Nextflow_File(Nextflow_Building_Blocks):
modules+=list(include.defines.values())
return modules
+ def get_calls_made_outside_of_main(self):
+ #Code without processes
+ code = self.get_code()
+ for proecess in self.processes:
+ code = code.replace(proecess.get_code(), "")
+ for sub in self.subworkflows:
+ code = code.replace(sub.get_code(), "")
+ for fun in self.functions:
+ code = code.replace(fun.get_code(), "")
+ if(self.first_file and self.main!=None):
+ code = code.replace(self.main.get_code(), "")
+ for include in self.includes:
+ code = code.replace(include.get_code(), "")
+
+ from .root import Root
+ self.root = Root(code=code, origin= self, modules_defined=self.get_modules_defined(), subworkflow_inputs = [])
+ self.root.initialise()
+ calls = {}
+ self.root.get_all_calls_in_subworkflow(calls=calls)
+ return list(calls.keys())
#----------------------
#INITIALISE
diff --git a/src/workflow.py b/src/workflow.py
index 277b1c7..1826ab7 100644
--- a/src/workflow.py
+++ b/src/workflow.py
@@ -461,21 +461,18 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
ankers = function_section+ "\n"*3 + process_section+ "\n"*3 + subworkflow_section
- to_replace = []
- for match in re.finditer(constant.FULL_INLCUDE_2, code):
- to_replace.append(match.group(0))
+
- if(to_replace==[]):
- pos_start = 0
- start_code_pattern = r"\#\!\s*\/usr\/bin\/env\s+nextflow"
- for match in re.finditer(start_code_pattern, code):
- pos_start = match.span(0)[1]+1
- code = code[:pos_start]+ankers+code[pos_start:]
- else:
- for r in to_replace:
- code = code.replace(r, ankers)
- ankers = ""
+ #Place ankers
+ pos_start = 0
+ start_code_pattern = r"\#\!\s*\/usr\/bin\/env\s+nextflow"
+ for match in re.finditer(start_code_pattern, code):
+ pos_start = match.span(0)[1]+1
+ code = code[:pos_start]+ankers+code[pos_start:]
+ #Remove the includes
+ for match in re.finditer(constant.FULL_INLCUDE_2, code):
+ code = re.sub(fr"{re.escape(match.group(0))}.*", "", code)
processes, subworkflows, functions = [], [], []
for c in self.get_workflow_main().get_all_calls_in_workflow():
@@ -488,6 +485,14 @@ George Marchment, Bryan Brancotte, Marie Schmit, Frédéric Lemoine, Sarah Cohen
functions.append(ele)
else:
raise Exception("This shoudn't happen")
+
+ #Get calls to functions made outside of themain which might have been imported -> so we need to add them
+ for c in self.get_first_file().get_calls_made_outside_of_main():
+ ele = c.get_first_element_called()
+ if(ele.get_type()=="Function"):
+ functions.append(ele)
+ else:
+ raise Exception("This shoudn't happen -> either a call to a process or subworkflow outside of main or subworkflow")
#Simplifying main
code = code.replace(self.get_workflow_main().get_code(get_OG = True), self.get_workflow_main().simplify_code())
--
GitLab