Blame Snakefile at 498b38c1a15e416b605e64743649ad32934bbb56

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be96d1b streamlineJeremy Magland 9 months ago1import yaml

3# Load session configuration

4with open("sessions.yaml", "r") as f:

5 config = yaml.safe_load(f)

7# Extract session information

8sessions = config["sessions"]

9session_ids = [s["session_id"] for s in sessions]

11# Define all targets

b565876 initialJeremy Magland 9 months ago12rule all:

13 input:

be96d1b streamlineJeremy Magland 9 months ago14 expand("figures/{session_id}.url", session_id=session_ids),

15 "index.md"

b565876 initialJeremy Magland 9 months ago16

be96d1b streamlineJeremy Magland 9 months ago17# Dynamic rule to create figures for each session

18rule create_figure:

b565876 initialJeremy Magland 9 months ago19 output:

be96d1b streamlineJeremy Magland 9 months ago20 "figures/{session_id}.url"

21 run:

22 # Find the session configuration

23 session = next(s for s in sessions if s["session_id"] == wildcards.session_id)

24 nwb_path = session["nwb_path"]

26 # Run the figure creation script

27 shell(f"python scripts/create_figure.py {nwb_path} {{output}}")

b565876 initialJeremy Magland 9 months ago28

be96d1b streamlineJeremy Magland 9 months ago29# Rule to generate index.md from template

30rule generate_index:

31 input:

32 expand("figures/{session_id}.url", session_id=session_ids),

33 "sessions.yaml",

34 "templates/index.md.jinja"

b565876 initialJeremy Magland 9 months ago35 output:

be96d1b streamlineJeremy Magland 9 months ago36 "index.md"

b565876 initialJeremy Magland 9 months ago37 shell:

be96d1b streamlineJeremy Magland 9 months ago38 "python scripts/generate_index.py"