Semantically, launch_dir should not be an output.

Declaring launch_dir as a directory() output is semantically incorrect. Snakemake outputs are artifacts produced by the rule, but launch_dir is merely a working directory where Nextflow runs. The .nextflow directory created inside it is the actual artifact.

Additionally, since the wrapper changes the working directory to launch_dir before running Nextflow, all relative paths (inputs, outputs, and the outdir param) will be resolved relative to some_directory instead of the Snakemake working directory. This means:

• output.multiqc_report declared as "results/multiqc/broadPeak/multiqc_report.html" will be created at "some_directory/results/multiqc/broadPeak/multiqc_report.html"
• Snakemake will look for it at "results/multiqc/broadPeak/multiqc_report.html" (relative to the Snakemake working directory)
• The test will fail with a missing output error

Consider these alternatives:

Option 1: Pre-create the directory and pass it as a param

 output:
     multiqc_report="results/multiqc/broadPeak/multiqc_report.html",
-    # directory from which nextflow is launched, will contain the `.nextflow` directory
-    launch_dir=directory("some_directory"),
 params:
     pipeline="nf-core/chipseq",
     revision="2.0.0",
     profile=["test", "docker"],
-    launch_dir=lambda wildcards, output: output.launch_dir,
+    launch_dir="some_directory",

Then add a rule to create the directory before running the test:

rule prepare_launch_dir:
    output:
        directory("some_directory")
    shell:
        "mkdir -p {output}"

Option 2: Make the wrapper convert paths to absolute before chdir

The wrapper should resolve all Snakemake input/output/params paths to absolute paths before changing directories, ensuring they remain valid after the chdir.

Run this script to verify whether the current implementation handles path resolution correctly:

🏁 Script executed:

#!/bin/bash
# Description: Check if the wrapper implementation handles path resolution after chdir

# Check if wrapper.py converts paths to absolute before chdir
rg -A 10 -B 5 'chdir.*launch_dir|os\.chdir' utils/nextflow/wrapper.py

Length of output: 263

Verify the outdir calculation after path resolution changes.

The calculation .parents[-2] correctly extracts "results" from the path. However, after the wrapper changes into launch_dir, this relative path needs to be handled correctly. Ensure that either:

1. The wrapper converts this param to an absolute path before chdir, or
2. The path is explicitly made relative to the new working directory

Run this script to check how the wrapper handles params that contain paths:

🏁 Script executed:

#!/bin/bash
# Description: Check if outdir and other path params are handled correctly after chdir

# Look for param handling around the chdir operation
rg -A 15 -B 5 'snakemake\.params' utils/nextflow/wrapper.py

Length of output: 1277

🏁 Script executed:

#!/bin/bash
# Locate add_parameter definition and inspect its behavior
rg -n 'def add_parameter' -A5 utils/nextflow/wrapper.py

Length of output: 0

🏁 Script executed:

#!/bin/bash
# Search for add_parameter definition and usage across the repo
rg -n "add_parameter" -n .

Length of output: 237