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Dev #615

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merged 10 commits into from
Aug 11, 2023
Merged

Dev #615

merged 10 commits into from
Aug 11, 2023

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a4000
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@a4000 a4000 commented Aug 8, 2023 •
edited by d4straub
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Addresses #612

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
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • 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 Aug 8, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4baba81

+| ✅ 152 tests passed       |+
#| ❔   3 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • readme - README did not have a Nextflow minimum version badge.
  • schema_lint - Parameter input is not defined in the correct subschema (input_output_options)

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-10 09:23:16

erikrikarddaniel
erikrikarddaniel approved these changes Aug 8, 2023
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Looks fine to me, but I know you discussed with @d4straub so maybe wait for another review from him.

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Now I see some tests fail because of updates with 2.9 tools. @d4straub updated to the new template yesterday.

a4000 and others added 4 commits August 8, 2023 14:15
d4straub
d4straub reviewed Aug 8, 2023
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That looks thorough, great!

Could you merge the recently added PR #614? That should solve the failing test nf-core linting / nf-core . nf-core linting / EditorConfig is caused by trailing whitespaces, you could avoid that by using VSC and nf-core extensions, if you wished to (or just take care manually). nf-core linting / PythonBlack can be solved by black.

d4straub
d4straub approved these changes Aug 10, 2023
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Looks good to me. Do you want to merge it?

modules/local/phyloseq.nf
TAX <- tax_table(tax_mat)
phy_obj <- phyloseq(OTU, TAX)

if (file.exists($sam_tsv)) {
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I am not aware of any example for conditional input that uses file.exists($file), so I am a little skeptic here. It might be working fine locally and on github, but we will need to see whether that works also on other systems. But easy enough to change in case it needs to be modified.

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That's a good point. I did my testing on a Linux server, but I'm hoping it would work on other systems.

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@a4000 a4000 merged commit ab5add3 into nf-core:dev Aug 11, 2023
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@a4000 @erikrikarddaniel @d4straub