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Add nf-core configs create sub command #2852

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Add nf-core configs create sub command #2852

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@jfy133 jfy133 commented Mar 18, 2024 •
edited

DO NOT USE THIS PR, THIS IS ONLY FOR REFERENCE PURPOSES -> STARTING FROM SCRATCH ON A SEPARATE PR

Closes #2731

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated

ewels and others added 30 commits August 21, 2023 00:15
@ewels
WIP: First stab at writing some Textual
513de95
@ewels
Refactor: Break into multiple files
0e8204e
@ewels
Remove unusued imports
e37d2e5
@mirpedrol
show error message when pressing enter
ee12eb5
@mirpedrol
show failure messages when button is pressed
dd18bcc
@mirpedrol
add usegenomicdata screen (TODO on_button_pressed)
486f180
@mirpedrol
add custom pipeline switch table to select pipeline features
5b8cfd5
@mirpedrol
create new widget PipelineFeature to display feature buttons and help…
0a40dab 
… text
@mirpedrol
add more custom features
39b9e3c
@mirpedrol
add template features to skip to TEMPLATE_CONFIG
25c9fa1
@mirpedrol
animate help box
610cbd9
@mirpedrol
add type_nfcore screen and use PipelineCreate to create a pipeline
6677144
@mirpedrol
modify PipelineCreate to accept a template dictionary
8bac0be
@mirpedrol
start modifying nf-core create command to use TUI and not CLI
43db7f6
@mirpedrol
small bug fixes and add a deprecation message for nf-core create command
99f426a
@mirpedrol
create command fails if one but not all arguments are provided
09bd5db
@mirpedrol
ask if launching TUI when using deprecated nf-core create command
9f121f7
@mirpedrol
add final_details screen for version and force
0c77029
@mirpedrol
add nfcorepipeline grid with features to select
bf9a541
@mirpedrol
first ask if the pipeline will be nf-core or custom before basicdetails
fec5e3e
@mirpedrol
use kwargs
0ef16b5
@mirpedrol
remove inexisten variable version from send-tweet github workflow
238767f
@mirpedrol
fix typo in gh_badges jinja variable to github_badges
7b4a342
@mirpedrol
bump version of nf-test snap files
b3fa25e
@mirpedrol
update changelog
6ff69b2
@mirpedrol
add outdir textinput and update config
17ba971
@mirpedrol
refactor jinja template 'branded' to 'is_nfcore'
0c64de8
@mirpedrol
refactor params_dict to jinja_params and use that instead of the config
7720117
@mirpedrol
refactor function obtain_jinja_params_dict
cb62be3
@mirpedrol
run create command from the App, mv nf_core/create.py to nf_core/pipe…
da1c68f 
…lines/create/create.py
@jfy133 jfy133 changed the base branch from master to dev March 18, 2024 08:32
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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 @jfy133,

It looks like this pull-request is has been made against the jfy133/nf-core-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 jfy133/nf-core-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!

@jfy133 jfy133 marked this pull request as draft March 18, 2024 08:32
jfy133 and others added 21 commits March 18, 2024 09:55
@jfy133
Add base command to main
8417de6
@jfy133
Rename to configs for consistency
12dacdd
@jfy133
Copy some basic structure from pipelinexcreate
650188f
@jfy133
We have a welcome screen!
e91dfa4
@jfy133
Fix help message
e144ad7
@jfy133
First question: infrastructure. Extra commit message courtesy of copi…
ea4e8ae 
…lot: The government has announced a $1.5 billion infrastructure package. What do you think of that? Is it enough? Is it the right kind of infrastructure? What would you do differently? And how would you pay for it?
@jfy133
Start adding basic details (confignameauthor,description), plus with …
6cb7485 
…custom text wdiget
@jfy133
Run basic details screen
5225fb7
@jfy133
Add infra type question (hpc or local))
b786e9c
@jfy133
Add github handle question for basic details
9ee8b43
@jfy133
Add infratype and env modules questions, rename basic details to nfco…
e69c536 
…re details
@jfy133
Add maxparams and other locations questions
3378340
@jfy133
Add misc. questions screen
62c0d2e
@jfy133
Initialise a basic config and attempt to update config
9fd60b1
@georgiesamaha
Add schedulertype question
6ee0088
@jfy133
Add validation for config github and URL
5788b14
@jfy133
Merge branch 'configbuilder' of github.com:jfy133/nf-core-tools into …
a2a1f51 
…configbuilder
@jfy133
Start adding further validation checks
d46f0b6
@jfy133
Add attempt for writing file for Julia to fix :Grimace:
8ce44c7
@mirpedrol
first test writing to a file
0ffbe8c
@jfy133
Add a self reminder here
37a2ed7
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New functionality: nf-core config create
4 participants
@jfy133 @ewels @mirpedrol @georgiesamaha