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Fix convert depths gzip #328

Merged
merged 5 commits into from
Aug 25, 2022
Merged

Fix convert depths gzip #328

merged 5 commits into from
Aug 25, 2022

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jfy133
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@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).

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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 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
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@jfy133 jfy133 changed the base branch from master to dev August 23, 2022 12:19
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jfy133 commented Aug 23, 2022

Trusting @apeltzer on this one ;)

jfy133
jfy133 commented Aug 23, 2022
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github-actions bot commented Aug 23, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 1414141

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

❗ 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
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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
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@d4straub d4straub d4straub approved these changes

@skrakau skrakau Awaiting requested review from skrakau

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