8000 Version 3.0 Release Candidate by chris-cheshire · Pull Request #159 · nf-core/cutandrun · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

Version 3.0 Release Candidate #159

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
Merged
merged 234 commits into from
Oct 27, 2022
Merged

Version 3.0 Release Candidate #159

merged 234 commits into from
Oct 27, 2022

Conversation

chris-cheshire
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/cutandrun 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).

chris-cheshire and others added 30 commits June 22, 2022 21:34
@chris-cheshire
Switched around statements for better error reporting in samplesheet
9baa428
@chris-cheshire
Added extra checks for blank lines in samplesheet
7bfc2ad
@chris-cheshire
Added line no to error samplesheet
d2a0f5c
@chris-cheshire
Added line strip to error check samplesheet
29f672a
@chris-cheshire
Increased memory for bedtools sort
fe9adc7
@chris-cheshire
Added resources for generate reports
1bdcd6b
@chris-cheshire
Bumped reporting resouces
52d4e86
@chris-cheshire
Updated macs2 results output to output all file types
fc716d5
@chris-cheshire
ebb4809 
Added better parameters for MACS2 and fixed error where only peak summits were
@chris-cheshire
fixed config error
d9624f7
@chris-cheshire
Added switches to stop warnings on resources
27e28cc
@chris-cheshire
Added secondary peaks into igv session
c77be02
@chris-cheshire
bugfix
80e157e
@chris-cheshire
Added new beds to igv
22290e1
@chris-cheshire
Removed warnings for indexes at init
7a2a9c2
@chris-cheshire
Added new macs2 parameters to schema
7ba04ba
@chris-cheshire
Updated schema
08c778e
@chris-cheshire
reenabled pipeline
951b2da
@chris-cheshire
igv now outputs narrowpeak
6a525a7
debugging
466d6cc
@chris-cheshire
igv will filter 0 size peak files
66c02b1
@chris-cheshire
Changed igv track write order
e5aa2b4
@chris-cheshire
white space
bbafa43
removing gunzip warning
a313d61
@chris-cheshire
igv fix
7f3e091
@chris-cheshire
igv fix
4344cef
@chris-cheshire
changed pipeline default to macs2
4b4e41c
deleted test data file
8f969ca
@chris-cheshire
downgraded email template
47fcc7e
@tamara-hodgetts
Merge pull request #9 from luslab/tamara-resources
2cc3fc6 
Tamara resources
alexthiery
alexthiery requested changes Oct 7, 2022
View reviewed changes
Copy link
Contributor
@alexthiery alexthiery left a comment

Choose a reason for hiding this comment

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

Mostly minor edits for the docs and typos. looking good

@maxulysse maxulysse changed the title Version 3.0 Release Canidate Version 3.0 Release Candidate Oct 24, 2022
maxulysse
maxulysse reviewed Oct 24, 2022
View reviewed changes
maxulysse
maxulysse reviewed Oct 24, 2022
View reviewed changes
Copy link
Member
@maxulysse maxulysse left a comment

Choose a reason for hiding this comment

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

Not sure I follow the convention for naming all the different test_*.yml files.
From what I can tell, you have the test_01... to test_06... all unique.
Then several test_verify_output_01... to test_verify_output_06....

@chris-cheshire
Copy link
Contributor Author

Not sure I follow the convention for naming all the different test_*.yml files. From what I can tell, you have the test_01... to test_06... all unique. Then several test_verify_output_01... to test_verify_output_06....

Its just so they appear in the order of the pipeline flow for different test types. It was getting very annoying trying to find the test that was executing!

alexthiery
alexthiery approved these changes Oct 24, 2022
View reviewed changes
Copy link
Contributor
@alexthiery alexthiery left a comment

Choose a reason for hiding this comment

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

looks good to me!

maxulysse
maxulysse approved these changes Oct 24, 2022
View reviewed changes
Copy link
Member
@maxulysse maxulysse left a comment

Choose a reason for hiding this comment

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

Congrats on the release

@chris-cheshire chris-cheshire merged commit dcaa442 into master Oct 27, 2022
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@maxulysse maxulysse maxulysse approved these changes

@alexthiery alexthiery alexthiery approved these changes

Assignees

@chris-cheshire chris-cheshire

Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
5 participants
@chris-cheshire @maxulysse @alexthiery @tamara-hodgetts @nf-core-bot
0