snakemake test

[Jiayi-Wang-Joey]

Snakemake run test and comparison report benchmark.

1. Need to modify some paths, otherwise got "No such directory..." error. Not sure if it is about the snakemake version or what? Maybe there is a better way to fix
2. Added two figures for count matrix comparisons

[Copilot]

Pull request overview

Updates the Snakemake pipeline’s method-comparison reporting and CWL/Singularity execution to support benchmarking runs without missing-path errors, and adds additional comparison visualizations.

Changes:

• Extend 02_comparison.Rmd with pseudo-bulk correlation plots and PCA visualizations (adds new R package usage).
• Adjust Snakemake to properly escape braces in an embedded Python heredoc and create a dedicated CWL_SINGULARITY_CACHE directory for CWL runs.
• Update conda environment and gitignore to support new reporting dependencies and generated artifacts.

Reviewed changes

Copilot reviewed 3 out of 4 changed files in this pull request and generated 3 comments.

File	Description
workflow/src/reports/02_comparison.Rmd	Adds pseudo-bulk correlation and PCA sections; introduces new package requirements and new plotting code.
workflow/envs/all_in_one.yaml	Adds r-ggh4x to support new faceting in the report.
workflow/Snakefile	Escapes braces in embedded Python and sets up a CWL Singularity cache directory to avoid missing-directory failures.
.gitignore	Ignores generated output and the new CWL cache directory; adds additional ignore patterns.

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[Copilot]

02_comparison.Rmd now loads/uses additional packages (e.g., pheatmap and scran::modelGeneVar). This conda env adds r-ggh4x but still doesn't include r-pheatmap or bioconductor-scran, so the report will fail at runtime. Please add the missing dependencies here (or remove the new imports if they aren't needed).

Suggested change

	- conda-forge::r-ggh4x
	- bioconda::bioconductor-biocgenerics
	- bioconda::bioconductor-biobase
	- conda-forge::r-ggh4x
	- conda-forge::r-pheatmap
	- bioconda::bioconductor-biocgenerics
	- bioconda::bioconductor-biobase
	- bioconda::bioconductor-scran

[Copilot]

This chunk header uses {r pb correlation, ...} which knitr will parse as label pb plus an (unknown) option correlation. If the intent is a single label, please rename to something without spaces (e.g., pb_correlation) to avoid knitr warnings and make chunk references unambiguous.

Suggested change

	```{r pb correlation, fig.width=12, fig.height=10}
	```{r pb_correlation, fig.width=12, fig.height=10}

[Copilot]

In this theme() call there are two issues that will break knitting: (1) panel.spacing = unit(...) will error unless unit is in scope (use grid::unit(...) or attach grid), and (2) there is a trailing comma after panel.border = ... which is a syntax error in R. Please fix both so the chunk runs.

Suggested change

	panel.spacing = unit(0.8, "lines"),
	aspect.ratio = 1,
	panel.border = element_rect(color = "black", fill = NA),
	panel.spacing = grid::unit(0.8, "lines"),
	aspect.ratio = 1,
	panel.border = element_rect(color = "black", fill = NA)