Nextflow

[dimalvovs]

• add functionality to run a standalone nextflow pipeline
• supports .h5ad and .rds files
• exposes all params via CLI, multiple npatterns can specified as comma-separated string e.g. 5,6,7

[Copilot]

Pull Request Overview

This PR adds support for running CoGAPS as a standalone Nextflow pipeline, handling both .h5ad and .rds inputs and exposing all parameters via the CLI (including multi-pattern support as comma-separated values).

• Updated nextflow.config defaults (including new n_top_genes) and resource limits.
• Enhanced main.nf to select top genes, refine distributed execution logic, and define a full example workflow for .h5ad/.rds.
• Updated documentation (README.md), R package version, CI ignore rules, and added .cirro configs.

Reviewed Changes

Copilot reviewed 9 out of 11 changed files in this pull request and generated 1 comment.

File	Description
nextflow.config	Tweaked default params, added n_top_genes, increased resources
main.nf	Gene selection, distributed params logic, workflow channels
README.md	Added Nextflow usage example and CLI param table
.Rbuildignore	Updated ignore rules for Nextflow, work/, main.nf, and .cirro

Comments suppressed due to low confidence (5)

README.md:38

• The input and outdir parameters are missing from this list. Adding them will help users understand how to specify input folders and output directory.

Supported CLI params and their defaults are:

main.nf:3

• The process label was changed to 'process_high' but there is no corresponding config block defining this label. Ensure 'process_high' is defined in nextflow.config or revert to a matching label.

  label 'process_high'

main.nf:62

• The closing brace here no longer matches an opening if since the guard was removed, causing a syntax error. Either restore the if (!is.null(dist_param)) wrapper or remove this stray }.

      };

main.nf:64

• Hardcoding outputFrequency = 100 ignores the user-specified niterations. Consider restoring floor($cparams.niterations/10) to align output frequency with iterations.

                             outputFrequency = 100);

main.nf:119

• This label was updated from 'process_low' to 'process_medium', but no matching config block appears to exist. Verify the label mapping in nextflow.config.

  label 'process_medium'

[Copilot]

nthreads is statically set to 1, so any CLI override of --nthreads will be ignored. Use params.nthreads instead of a hardcoded value.

Suggested change

	ch_fixed_params = Channel.of([niterations: params.niterations, sparse: params.sparse, distributed: params.distributed, nsets:params.nsets, nthreads:1])
	ch_fixed_params = Channel.of([niterations: params.niterations, sparse: params.sparse, distributed: params.distributed, nsets:params.nsets, nthreads: params.nthreads])

[dimalvovs]

nthreads is tricky (works with multithreaded only) and never used, would prefer leaving it hardcoded

[drbergman]

Can't say I can understand all the details of the changes here, but I think supporting easily running cogaps with multiple pattern numbers is worthy of incrementing the minor version.

Would it also be worth it to support range expression for npatterns? e.g. npatterns=5:5:20? A function to parse this string should be straightforward.

[drbergman]

Certainly this PR is worthy of a minor increment!