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.

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

Add customisation option to remove all GitHub support with nf-core create #1766

Merged
merged 22 commits into from
Aug 29, 2022
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
22 commits
Select commit Hold shift + click to select a range
708a9b0
add option to remove git hosting from pipeline template
mirpedrol Aug 25, 2022
a6d223e
add file bug_report.yml to files_exist when github hosting is not add…
mirpedrol Aug 25, 2022
8b7e1b1
update CHANGELOG
mirpedrol Aug 25, 2022
2277d2e
Merge branch 'dev' into no-git
mirpedrol Aug 25, 2022
cff1717
Generate new screengrabs with rich-codex
github-actions[bot] Aug 25, 2022
21565bd
disable progress bars in `nf-core (modules) lint` with `--hide-progress`
Aug 25, 2022
103325a
Generate new screengrabs with rich-codex
github-actions[bot] Aug 25, 2022
d55f089
fix argument order
Aug 25, 2022
6d020ae
Merge branch 'disable-lint-progress-bar' of https://github.com/masheh…
Aug 25, 2022
65735ea
update readme
Aug 25, 2022
1619574
Generate new screengrabs with rich-codex
github-actions[bot] Aug 25, 2022
cf31f5e
enable env variables for options, move hide-progress into decorator g…
Aug 29, 2022
39caa9f
Merge branch 'disable-lint-progress-bar' of https://github.com/masheh…
Aug 29, 2022
e30ebb4
include #1765 in this PR
mashehu Aug 29, 2022
f4449ea
Generate new screengrabs with rich-codex
github-actions[bot] Aug 29, 2022
6df2717
Merge pull request #1769 from mashehu/disable-lint-progress-bar
mashehu Aug 29, 2022
8a2317b
add option to remove git hosting from pipeline template
mirpedrol Aug 25, 2022
1980d81
add file bug_report.yml to files_exist when github hosting is not add…
mirpedrol Aug 25, 2022
1e3efde
update CHANGELOG
mirpedrol Aug 25, 2022
0597be6
merge conflicts
mirpedrol Aug 29, 2022
e64d248
merge conflicts
mirpedrol Aug 29, 2022
4ce9a75
Generate new screengrabs with rich-codex
github-actions[bot] Aug 29, 2022
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
12 changes: 10 additions & 2 deletions .github/workflows/rich-codex.yml
Original file line number Diff line number Diff line change
@@ -1,5 +1,10 @@
name: Generate images for docs
on: [push]
on:
push:
branches-ignore:
- "master"
- "dev"
workflow_dispatch:
jobs:
rich_codex:
runs-on: ubuntu-latest
Expand All @@ -22,6 +27,10 @@ jobs:

- name: Generate terminal images with rich-codex
uses: ewels/rich-codex@v1
env:
COLUMNS: 100
NFCORE_LINT_HIDE_PROGRESS: true
NFCORE_MODULES_LINT_HIDE_PROGRESS: true
with:
commit_changes: "true"
clean_img_paths: docs/images/*.svg
Expand All @@ -31,4 +40,3 @@ jobs:
which nf-core &&
nextflow -version &&
nf-core --version
PY_COLORS=true
2 changes: 2 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -13,6 +13,7 @@
- Make `nf-core create` fail if Git default branch name is dev or TEMPLATE ([#1705](https://github.com/nf-core/tools/pull/1705))
- Convert `console` snippets to `bash` snippets in the template where applicable ([#1729](https://github.com/nf-core/tools/pull/1729))
- Add `branch` field to module entries in `modules.json` to record what branch a module was installed from ([#1728](https://github.com/nf-core/tools/issues/1728))
- Add customisation option to remove all GitHub support with `nf-core create` ([#1766](https://github.com/nf-core/tools/pull/1766))

### Linting

Expand Down Expand Up @@ -49,6 +50,7 @@
- Replace use of the deprecated `distutils` Version object with that from `packaging` ([#1735](https://github.com/nf-core/tools/pull/1735))
- Add code to cancel CI run if a new run starts ([#1760](https://github.com/nf-core/tools/pull/1760))
- CI for the API docs generation now uses the ubuntu-latest base image ([#1762](https://github.com/nf-core/tools/pull/1762))
- Add option to hide progress bars in `nf-core lint` and `nf-core modules lint` with `--hide-progress`.

### Modules

Expand Down
4 changes: 4 additions & 0 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -287,6 +287,10 @@ working_dir: tmp

Once downloaded, you will see something like the following file structure for the downloaded pipeline:

<!-- RICH-CODEX
working_dir: tmp
-->

![`tree -L 2 nf-core-rnaseq/`](docs/images/nf-core-download-tree.svg)

You can run the pipeline by simply providing the directory path for the `workflow` folder to your `nextflow run` command:
Expand Down
128 changes: 64 additions & 64 deletions docs/images/nf-core-bump-version.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
218 changes: 95 additions & 123 deletions docs/images/nf-core-create.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
152 changes: 136 additions & 16 deletions docs/images/nf-core-download-tree.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
126 changes: 63 additions & 63 deletions docs/images/nf-core-download.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
118 changes: 59 additions & 59 deletions docs/images/nf-core-launch-rnaseq.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
194 changes: 95 additions & 99 deletions docs/images/nf-core-licences.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
368 changes: 141 additions & 227 deletions docs/images/nf-core-lint.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
170 changes: 85 additions & 85 deletions docs/images/nf-core-list-rna.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
148 changes: 74 additions & 74 deletions docs/images/nf-core-list-stars.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
154 changes: 77 additions & 77 deletions docs/images/nf-core-list.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
152 changes: 76 additions & 76 deletions docs/images/nf-core-modules-bump-version.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
184 changes: 86 additions & 98 deletions docs/images/nf-core-modules-create-test.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
196 changes: 90 additions & 106 deletions docs/images/nf-core-modules-create.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
312 changes: 150 additions & 162 deletions docs/images/nf-core-modules-info.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
116 changes: 58 additions & 58 deletions docs/images/nf-core-modules-install.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
310 changes: 112 additions & 198 deletions docs/images/nf-core-modules-lint.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
190 changes: 95 additions & 95 deletions docs/images/nf-core-modules-list-local.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
190 changes: 95 additions & 95 deletions docs/images/nf-core-modules-list-remote.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
116 changes: 56 additions & 60 deletions docs/images/nf-core-modules-mulled.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
214 changes: 105 additions & 109 deletions docs/images/nf-core-modules-patch.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
102 changes: 51 additions & 51 deletions docs/images/nf-core-modules-remove.svg
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading