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Fix CENTRIFUGE header modification when --out-fmt turned on #338

Merged
merged 4 commits into from
Jul 28, 2023
Merged

Fix CENTRIFUGE header modification when --out-fmt turned on #338

merged 4 commits into from
Jul 28, 2023

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jfy133
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@jfy133 jfy133 commented Jul 27, 2023

closes #337

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/taxprofiler 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).

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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/taxprofiler 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/taxprofiler 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 changed the base branch from master to dev July 27, 2023 12:00
@jfy133 jfy133 requested a review from a team July 27, 2023 12:01
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github-actions bot commented Jul 27, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 3437201

+| ✅ 157 tests passed       |+
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in methods_description_template.yml: #Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-27 13:11:06

LilyAnderssonLee
LilyAnderssonLee approved these changes Jul 27, 2023
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@LilyAnderssonLee
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You need to change the line 242 of profiler.nf
from
ch_input_for_centrifuge_kreport = CENTRIFUGE_CENTRIFUGE.out.report
to
ch_input_for_centrifuge_kreport = CENTRIFUGE_CENTRIFUGE.out.results

So basically use results.txt as input of kreport.

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I have run my analysis based on these new changes and it worked perfectly. You can go ahead and merge it.

@jfy133 jfy133 merged commit fba2d8c into dev Jul 28, 2023
20 checks passed
@jfy133 jfy133 deleted the centrifuge-fix branch July 28, 2023 08:11
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Successfully merging this pull request may close these issues.

CENTRIFUGE produces a wrong, kraken-like report by mistakenly using the report.txt file
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@jfy133 @LilyAnderssonLee