Skip to content

Fix convert depths gzip#328

Merged
jfy133 merged 5 commits intodevfrom
fix-convert-depths-gzip
Aug 25, 2022
Merged

Fix convert depths gzip#328
jfy133 merged 5 commits intodevfrom
fix-convert-depths-gzip

Conversation

@jfy133
Copy link
Copy Markdown
Member

@jfy133 jfy133 commented Aug 23, 2022

To close #327

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/mag 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.
  • [ x] README.md is updated (including new tool citations and authors/contributors).

@github-actions
Copy link
Copy Markdown

github-actions Bot commented Aug 23, 2022

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 nf-core/mag 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 nf-core/mag 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 commented Aug 23, 2022
View reviewed changes
Comment thread CHANGELOG.md Outdated
@jfy133 jfy133 changed the base branch from master to dev August 23, 2022 12:19
@jfy133
Copy link
Copy Markdown
Member Author

jfy133 commented Aug 23, 2022

Trusting @apeltzer on this one ;)

jfy133
jfy133 commented Aug 23, 2022
View reviewed changes
Comment thread CHANGELOG.md Outdated
@github-actions
Copy link
Copy Markdown

github-actions Bot commented Aug 23, 2022 •
edited
Loading

nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1414141

+| ✅ 147 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-08-25 07:15:13

@jfy133 jfy133 requested review from d4straub and skrakau and removed request for d4straub August 24, 2022 13:19
d4straub
d4straub approved these changes Aug 24, 2022
View reviewed changes
Copy link
Copy Markdown
Collaborator

@d4straub d4straub 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 whether that works, I have the description:
-f, --force force overwrite of output file and compress links
but fine to me

@jfy133 jfy133 merged commit 6d26d5e into dev Aug 25, 2022
@jfy133 jfy133 deleted the fix-convert-depths-gzip branch August 25, 2022 08:06
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Reviewers

@d4straub d4straub d4straub approved these changes

@skrakau skrakau Awaiting requested review from skrakau

Assignees

No one assigned

Labels

None yet

Projects

None yet

Milestone

No milestone

Development

Successfully merging this pull request may close these issues.

gzip: ...: Too many levels of symbolic links

2 participants

@jfy133 @d4straub