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version fix #78

Merged
merged 57 commits into from
Mar 4, 2022
Merged

version fix #78

merged 57 commits into from
Mar 4, 2022

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daichengxin
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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/quantms 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).
  • 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).

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github-actions bot commented Feb 18, 2022 •
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nf-core lint overall result: Passed ✅

Posted for pipeline commit 3c0991d

+| ✅ 137 tests passed       |+
#| ❔   3 tests were ignored |#

❔ Tests ignored:

  • files_exist - File is ignored: conf/igenomes.config
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.2
  • Run at 2022-03-04 02:26:59

@jpfeuffer
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The version has to be 11 otherwise markdown linting fails

@daichengxin
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The version has to be 11 otherwise markdown linting fails

ok. I am removing functions.nf

@jpfeuffer
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There is probably a way to ignore tests in the nf-core linting. We should ignore the markdown linting.yml until this is fixed by them.

@daichengxin
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The code to determine whether it is tmt or lfq needs to be changed. Honestly, it's a bit difficult. Because the value in the DataflowStream object cannot be extracted

@jpfeuffer
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How do you mean? Can you post links to the code?

@jpfeuffer
remove dependency on labelling type in config.
d71180d 
this is handled by the "withName" attribute anyway
@ypriverol ypriverol self-requested a review February 28, 2022 14:42
@jpfeuffer
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@daichengxin Can you fix pMultiQC such that it reads ISO or LFQ from the mztab if that parameter is not given? Should be one of the entries in the mztab metadata.

@daichengxin
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@daichengxin Can you fix pMultiQC such that it reads ISO or LFQ from the mztab if that parameter is not given? Should be one of the entries in the mztab metadata.

ok, I am updating it.

@jpfeuffer
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What do you think? Ready to merge?

This was referenced Mar 4, 2022
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@ypriverol ypriverol merged commit 6b8b992 into bigbio:dev Mar 4, 2022
ypriverol added a commit that referenced this pull request Mar 20, 2023
@ypriverol
Merge pull request #78 from ypriverol/dev
dd22683 
small format changes
This pull request was closed.
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@ypriverol ypriverol ypriverol approved these changes

@jpfeuffer jpfeuffer jpfeuffer approved these changes

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3 participants
@daichengxin @jpfeuffer @ypriverol