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Add new command nf-core rocrate to create a Research Object crate for a pipeline #2679

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wants to merge 174 commits into from
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Add new command nf-core rocrate to create a Research Object crate for a pipeline #2679

wants to merge 174 commits into from

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mashehu
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@mashehu mashehu commented Jan 23, 2024

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mashehu and others added 30 commits December 5, 2022 11:46
@mashehu
add conda channel order to nextflow.config template
a1e6412
@mashehu @maxulysse
Update nf_core/pipeline-template/nextflow.config
a023d6e 
Co-authored-by: Maxime U. Garcia <[email protected]>
@maxulysse
Merge branch 'dev' into add-conda-defaults
4d01080
@renovate
Update SamKirkland/FTP-Deploy-Action action to v4.3.4
099443f
@renovate
Update actions/checkout action to v4
85f311a
@renovate
Update actions/stale action to v9
3de1dcf
@renovate
Update actions/upload-artifact action to v4
0833e89
@renovate
Update zentered/bluesky-post-action action to v0.1.0
2576060
@mashehu
bump to 2.12dev
7831f7a
@mashehu
Merge pull request nf-core#2617 from mashehu/bump-to-dev
9bdf7c9 
Bump to 2.12dev
@MatthiasZepper
Add a Github Action Workflow to the pipeline template that tests a su…
6ea4d62 
…ccessful download.
@mirpedrol
add ruff formatter and linter
998a22c
@mirpedrol
remove isort
9fdcf03
@mirpedrol
remove python black
418f0be
@mirpedrol
remove pyupgrade
2ca9b19
@mirpedrol
update CONTRIBUTING.md
c25c5be
@mirpedrol
select import sorting and run first linter and then formatter
e40f7b9
@mirpedrol
ignore import checks in __init__.py files
df3d3a1
@mirpedrol
run ruff check --fix
14ca618
@mirpedrol
manually fix other ruff errors
8cc98a2
@mirpedrol
remove unused fullname from SyncedRepo and fix circular import
f2f3645
@mirpedrol
locate ruff cache dir at ~/.cache/ruff
3579de6
@mirpedrol
Apply suggestions from code review
691e654
@mirpedrol
use required to create params file
aaa5166
@sateeshperi
fix positional input in template
5419aad
@mashehu
don't run prettier on things handled by ruff
b430bbf
@mashehu
don't migrate empty config files to nf-test
4d187fd
@mashehu
handle stageAs in input parsing correctly
9587aab 
closes nf-core#2622
@mashehu
fix variable name
855b254
@mashehu
Automatically create changelog entries from PRs
44683c5 
code taken from MultiQC and customized for our use case
edmundmiller and others added 28 commits January 9, 2024 08:38
@edmundmiller
ci(renovate): Ignore modules in pipeline template
14f594c 
nf-core/ops#29
@edmundmiller
chore: Update Changelog
9cfea63
@edmundmiller
Merge pull request nf-core#2648 from nf-core/renovate-docker
a54686b
@mashehu
fix ignorepath
dcbced8
@nf-core-bot
[automated] Update CHANGELOG.md [no ci]
28de3d6
@mashehu
avoid stopping all CI tests with changelog action
891746d
@mashehu
Merge branch 'fix-renovate' of github.com:mashehu/tools into fix-reno…
0c79f65 
…vate
@mashehu
update changelog
7538d7e
@mashehu
Merge pull request nf-core#2651 from mashehu/fix-renovate
6f85c0a 
fix ignorepath
@mashehu
more renovate fixes [no changelog]
cf73506
@nf-core-bot
[automated] Update CHANGELOG.md
a7e1533
@mashehu
Update CHANGELOG.md
02fe413
@mashehu
Merge pull request nf-core#2652 from mashehu/fix-renovate
ed15dd3 
more renovate fixes
@ewels
Add Trogon
8320f80 
Signed-off-by: Phil Ewels <[email protected]>
@ewels
Fix ruff linting
41a6164
@renovate
Update pre-commit hook astral-sh/ruff-pre-commit to v0.1.12
81a8c08
@nf-core-bot
[automated] Update CHANGELOG.md
900ce78
@mashehu
Update CHANGELOG.md
8b760dd
@mashehu
Merge pull request nf-core#2657 from nf-core/renovate/astral-sh-ruff-…
39a52d5 
…pre-commit-0.x
@ewels
add to changelog
a31fa1f
@ewels
Add to the readme
a616de2
@ewels
Merge pull request nf-core#2655 from ewels/trogon
669be1e 
Add support for Click TUI with Trogon
@renovate
Update pre-commit hook astral-sh/ruff-pre-commit to v0.1.13
56e7734
@nf-core-bot
[automated] Update CHANGELOG.md
91ae4fc
@mashehu
Merge pull request nf-core#2660 from nf-core/renovate/astral-sh-ruff-…
110d99f 
…pre-commit-0.x
@mashehu
second attempt to add ro crates
e7249b7
@mashehu
fix import
a597c8c
@mashehu
first running version
7a66e06
@github-actions GitHub Actions
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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @mashehu,

It looks like this pull-request is has been made against the mashehu/tools master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the mashehu/tools dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@mashehu mashehu closed this Jan 23, 2024
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8 participants
@mashehu @maxulysse @MatthiasZepper @mirpedrol @sateeshperi @nf-core-bot @edmundmiller @ewels