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nf-validation on samplesheet #88

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Merged
Daniel-VM merged 4 commits into from
Sep 23, 2023
Merged

nf-validation on samplesheet #88

Daniel-VM merged 4 commits into from
Sep 23, 2023

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@Daniel-VM Daniel-VM commented Sep 22, 2023

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/bacass 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).

PR description

Added nf-validation on sample sheet (#87). It enables the parsing of input sample sheets in various formats, including TSV, CSV, and YAML files.

Now, INPUT_CHECK() subworfklow is no longer requiered.

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github-actions bot commented Sep 22, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 8ba1df5

+| ✅ 156 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   4 tests had warnings |!
Details

❗ Test warnings:

  • pipeline_todos - TODO string in README.md: Describe the minimum required steps to execute the pipeline, e.g. how to prepare samplesheets.
  • pipeline_todos - TODO string in README.md: update the following command to include all required parameters for a minimal example
  • 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
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-09-22 14:20:23

@Daniel-VM Daniel-VM requested a review from d4straub September 22, 2023 10:36
d4straub
d4straub reviewed Sep 22, 2023
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d4straub
d4straub reviewed Sep 22, 2023
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d4straub
d4straub reviewed Sep 22, 2023
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d4straub approved these changes Sep 22, 2023
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Looks good to me!
I give my ok here before all tests succeeded, please wait until those are all fine.

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d4straub commented Sep 22, 2023

I spotted two warnings in the tests:

WARN: A process with name 'MINIMAP2_CONSENSUS' is defined more than once in module script: /home/runner/work/bacass/bacass/./workflows/bacass.nf -- Make sure to not define the same function as process
WARN: A process with name 'MINIMAP2_POLISH' is defined more than once in module script: /home/runner/work/bacass/bacass/./workflows/bacass.nf -- Make sure to not define the same function as process

that can be easily removed by importing those processes under different names. Maybe for another PR.

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Daniel-VM commented Sep 23, 2023

Great!!. Thanks for the review.

Concerning the warnings, I've been unable to replicate them when running nextflow run main.nf --profile docker,test_long --ourdir ./results locally (nextflow v23.04.1 ). I could be wrong, but I have not found MINIMAP2_CONSENSUS() or MINIMAP2_POLISH() being invoked twice or more within the 'workflows/bacass.nf' file.

I will test it further and do another PR.

@Daniel-VM Daniel-VM merged commit 463d4b0 into nf-core:dev Sep 23, 2023
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