Walkthrough

This pull request refines the processing of wildcards by modifying the handling of callable items in the Snakemake rules. In the _apply_wildcards method, the assignment and condition checking for callable items have been adjusted, with an update to the concretize call. The expand_input method is similarly updated to pass along callable flags. Additionally, new functions have been introduced in the test Snakefile to dynamically generate input filenames for rules based on wildcards.

Changes

Sequence Diagram(s)

sequenceDiagram
    participant Caller
    participant Rule
    participant Concretize

    Caller->>Rule: call _apply_wildcards(newitems, olditems, wildcards)
    Note right of Rule: Check if item is callable
    alt Item is callable
        Rule->>Rule: Assign olditem to from_callable
    else Item is not callable
        Rule->>Rule: Set from_callable to None
    end
    Rule->>Rule: Check if from_callable is not None
    Rule->>Concretize: Call concretize(from_callable)
    Concretize-->>Rule: Return processed result
    Rule-->>Caller: Return updated wildcards

sequenceDiagram
    participant RuleE
    participant Snakefile
    participant GetE

    RuleE->>Snakefile: Request input for rule e
    Snakefile->>GetE: call get_e_input(wildcards)
    GetE-->>Snakefile: return input filename
    Snakefile-->>RuleE: Provide dynamic input filename

sequenceDiagram
    participant RuleF
    participant Snakefile
    participant GetF

    RuleF->>Snakefile: Request input for rule f
    Snakefile->>GetF: call get_f_input(wildcards)
    GetF-->>Snakefile: return input filename
    Snakefile-->>RuleF: Provide dynamic input filename

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