Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Chore/update readme #99

Merged
merged 3 commits into from
Jun 24, 2024
Merged

Chore/update readme #99

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
98238c8
fix: add layour docs to readme
ambarrio Jun 20, 2024
141642a
fix: changelog
ambarrio Jun 20, 2024
bfe93c4
fix: update output layout step
ambarrio Jun 20, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,6 +9,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

- [[PR #96](https://github.com/nf-core/pixelator/pull/96)] - Make all ext.args assignments closures
- [[PR #98](https://github.com/nf-core/pixelator/pull/98)] - Update metromap to include layout step
- [[PR #99](https://github.com/nf-core/pixelator/pull/99)] - Update README to include layout step

### Software dependencies

Expand Down
3 changes: 2 additions & 1 deletion README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,8 @@ It takes a samplesheet as input and will process your data using `pixelator` to
5. Compute the components of the graph from the edge list in order to create putative cells ([`pixelator graph`](https://github.com/PixelgenTechnologies/pixelator))
6. Call and annotate cells ([`pixelator annotate`](https://github.com/PixelgenTechnologies/pixelator))
7. Analyze the cells for polarization and colocalization ([`pixelator analysis`](https://github.com/PixelgenTechnologies/pixelator))
8. Report generation ([`pixelator report`](https://github.com/PixelgenTechnologies/pixelator))
8. Generate 3D graph layouts for visualization of cells ([`pixelator layout`](https://github.com/PixelgenTechnologies/pixelator))
9. Report generation ([`pixelator report`](https://github.com/PixelgenTechnologies/pixelator))

> [!WARNING]
> Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity.
Expand Down
1 change: 1 addition & 0 deletions docs/output.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ The pipeline consists of the following steps:
- [Compute connected components](#compute-connected-components)
- [Filtering, annotation, cell-calling](#cell-calling-filtering-and-annotation)
- [Downstream analysis](#downstream-analysis)
- [Generate layouts for visualization](#compute-layouts-for-visualization)
- [Generate reports](#generate-reports)

### Preprocessing
Expand Down