Handling cases in Nextflow #74
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# Conflicts: # probe_src/python/probe_py/manual/cli.py
charmoniumQ
reviewed
Dec 7, 2024
| @@ -139,7 +235,16 @@ def create_processes(self) -> None: | |||
| inputs = [n for n in self.graph.predecessors(node) if isinstance(n, FileNode)] | |||
| outputs = [n for n in self.graph.successors(node) if isinstance(n, FileNode)] | |||
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| if self.is_standard_case(node, inputs, outputs) : | |||
| # Skip any command that calls another script | |||
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We need a more general way (in a different PR) of handing the case where process forks child processes than asking if the command was sh. There are many other commands that do this, make, bash, ..., any command could do this.
We should analyze this by the tree structure (later on).
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Cases that should
PROBEhandle when exportingNextflow:One Input, One Output
Multiple Inputs, One Output
Inline Commands: Inline commands that directly modify the input file (e.g., using sed, awk, or similar)
Chained Scripts: If a process node calls another script
No Input Command: Commands like
ls .: Commands that don't take an explicit input file but generate outputMultiple Inputs, Multiple Outputs
Ensure that any environment variables or context-specific settings are captured and translated into the Nextflow environment