We are chuffed to provide some updates and improvements to EPI2ME Desktop, wf-human-variation and wf-single-cell. Highlights include a selection of updates to wf-single-cell that improve workflow stability, compatibility, and resource usage, and an update to modkit in wf-human varaiton decreasing run time when the --mod subworkflow is enabled.

New releases:

EPI2ME Desktop v5.3.1
- Fixed resource bars in app not matching values set in docker (macos)
- Fixed disk usage panel not working on windows
- Fixed installation of some workflows where data was not being unpacked while installing workflows (note: this will not repair workflows that were previously unpacked incorrectly)
- Fixed NF core workflows not loading correctly due to manifest changes
wf-human-varation v2.8.0
- Updated modkit to run base modification processes up to 10x faster, decreasing the total time to run the workflow with the --mod subworkflow enabled.
- Added bigWig files as an output for 5mC base modifications to allow efficient visualisation.
- Fixed a misleading error about basecaller model detection when input data is below the required coverage threshold.
wf-single-cell v3.3.4
- Added new workflow diagram to the documentation.
- Visium HD workflow now accepts compressed reference inputs.
- Fixed missing quality strings in visium HD output BAMs and summary TSVs.
- Fixed excessive memory usage issue in the catr_tags_by_chrom process.
- Fixed error during UMAP generation caused by low cell count.
wf-metagenomics v2.14.2 + wf-16s v1.6.1
- Added Greengenes2 database: the database used in the recent ZymoBIOMICS Microbial Communities with 16S dataset blog post is now available as “Greengenes2_plus”.
- Added Workflow overview diagram in the documentation.
- Added Comprehensive database reference table to the README with citations and resource links.
- Fixed Missing ranks when the user-selected taxonomic_rank was deeper than the maximum rank available for a given taxon in the database.

FAQ: How do I make a community Nextflow workflows work in EPI2ME Desktop?

Some community workflows are valid Nextflow pipelines but do not fully meet EPI2ME Desktop’s metadata validation requirements. In these cases, you need to adjust the workflow’s metadata. This affects EPI2ME Desktop versions 5.3.0 and higher.

Required steps

Update the manifest section in nextflow.config Ensure the manifest metadata matches the GitHub repository:
- name must match <author>/<repo-name>
- author must match <author>
  For example, for: https://github.com/example-author/example-workflow the manifest should include:

manifest 
        name = 'example-author/example-workflow'
        author = 'example-author'

Use semantic versioning for the workflow version EPI2ME Desktop requires the workflow version field to use semantic versioning, including major, minor, and patch numbers.
- For example: v1.2 → v1.2.01.2 → 1.2.0
Use a lowercase repository path on Ubuntu/Unix
- When running EPI2ME Desktop on Ubuntu or Unix-based systems, workflows may fail to import if the GitHub repository path contains capital letters.
  - For example, this repository path may not import correctly because the owner contains capital letters: https://github.com/Example-Author/example-workflow
  - Use a fork or repository path where the owner and repository name are lowercase: https://github.com/example-author/example-workflow
Ensure the README file is named README.md
- The workflow repository must contain a README file named exactly: README.md
Import your fork into EPI2ME Desktop
- Import the workflow using the repository URL in this format: https://github.com/<author>/<repo-name> Do not use URLs containing /tree/ or /blob/.
  - For example, use: https://github.com/example-author/example-workflow
  - Do not use: https://github.com/example-author/example-workflow/tree/mainhttps://github.com/example-author/example-workflow/blob/main/nextflow.config