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

Jump to bottom

Dev > Master for v2.0.0 #41

Merged
merged 234 commits into from
Jul 5, 2023
Merged

Dev > Master for v2.0.0 #41

merged 234 commits into from
Jul 5, 2023

Conversation

LaurenceKuhl
Copy link
Contributor

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs- [ ] If necessary, also make a PR on the nf-core/crisprseq branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

nf-core-bot and others added 30 commits December 19, 2022 12:05
@nf-core-bot
Template update for nf-core/tools version 2.7.2
dccf735
@mirpedrol
bump to 1.0dev
fea8464
@mirpedrol
add Zenodo DOI
2e3a584
@mirpedrol
add Zenodo badge
8ad61b5
@mirpedrol
run prettier
ee17129
@mirpedrol
Merge pull request #14 from nf-core/master
c2c3347 
Add Zenodo DOI master -> dev
@LaurenceKuhl
Fastqc and first mageck module
8f3a4b0
@LaurenceKuhl
Added mageck test and mageck count
6e9139f
@mirpedrol
add extract umi step
760fa55
@mirpedrol
add test_umis.config
21cda6b
@LaurenceKuhl
First version of the screening subworkflow and working
848b2f2
@LaurenceKuhl
Added a line in the modules.config so it's sample separated in mageck…
4efe4c3 
… mle results
@mirpedrol
fix extract_umis
373b809
@mirpedrol
install vsearch
ab49b68
@mirpedrol
add vsearch/cluster step
1eb72b8
@mirpedrol
don't compress cluster fastas
8467cd9
@mirpedrol
add closure to obtain sequence from umi
bc43a97
@mirpedrol
try to make umi_to_sequence.py faster
181c3d5
@mirpedrol
use a groovy function for umi_to_sequence
2198371
@mirpedrol
install vsearch/sort
828dbf5
@mirpedrol
add umi_bin_size parameter
731ffb3
@mirpedrol
update vsearch/sort and add sequence obtention from umi
46535d8
@mirpedrol
add first minimap step for UMI consensus
75584e2
@mirpedrol
install new module racon
4199628
@mirpedrol
add racon
e9adce8
@LaurenceKuhl
Functioning complete pipeline
4b9d825
@nf-core-bot
Template update for nf-core/tools version 2.8
c9e8726
@LaurenceKuhl
Fully functionning pipeline
90b6ea6
@mirpedrol
Merge branch 'dev' into bump-1.0dev
2396278
@mirpedrol
Merge pull request #13 from mirpedrol/bump-1.0dev
140a77d 
Bump to 1.1dev
SusiJo
SusiJo approved these changes Jun 28, 2023
View reviewed changes
Copy link
Contributor

@SusiJo SusiJo left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Just dropped some minor suggestions and corrections. Looks very next level to me 💯 🚀

jianhong
jianhong reviewed Jun 29, 2023
View reviewed changes
conf/modules.config Outdated Show resolved Hide resolved
jianhong
jianhong reviewed Jun 29, 2023
View reviewed changes
conf/modules.config Outdated Show resolved Hide resolved
@mirpedrol
Copy link
Member

Hi @jianhong, we addressed the comments :) are you happy to approve?

Note: linting is not failing due to the last nf-core/tools release to v2.9. They pass with v2.8. Already added the template update to the next milestone for crisprseq v2.1.0 to not overload this release with too many changes.

jianhong
jianhong approved these changes Jul 3, 2023
View reviewed changes
Copy link

@jianhong jianhong left a comment

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

LGTM.

@LaurenceKuhl LaurenceKuhl merged commit a797392 into master Jul 5, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@SusiJo SusiJo SusiJo approved these changes

@mirpedrol mirpedrol mirpedrol left review comments

@jianhong jianhong jianhong approved these changes

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
6 participants
@LaurenceKuhl @mirpedrol @jianhong @SusiJo @nf-core-bot @mashehu