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Fixed S3 bucket path in conditional statements #124

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Merged
maxulysse merged 3 commits into from
Feb 12, 2024
Merged

Fixed S3 bucket path in conditional statements #124

maxulysse merged 3 commits into from
Feb 12, 2024

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@nschcolnicov
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@nschcolnicov nschcolnicov commented Feb 8, 2024 •
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Fixed the issue reported here: #121
It was a simple fix, the conditional statement wasn't working because it was missing a "/" to match the one defined in the nextflow.config, so the snpEff cache data dir wasn't being built properly.

To test it I ran the command: nextflow run ../../main.nf -profile test,docker --annotate_tools snpeff --outdir . -resume --download_cache

image

@maxulysse There are two more issues that I spotted that the publishDir for snpEff and VEP contain a null value, I will create an issue for this address it on a separate PR

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/rnavar branch on the nf-core/test-datasets repository.
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github-actions bot commented Feb 8, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit a42bb7e

+| ✅ 188 tests passed       |+
!| ❗   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 awsfulltest.yml: You can customise AWS full pipeline tests as required
  • pipeline_todos - TODO string in WorkflowRnavar.groovy: Optionally add in-text citation tools to this list.
  • 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 2.12.1
  • Run at 2024-02-12 09:33:15

@nschcolnicov nschcolnicov mentioned this pull request Feb 8, 2024
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maxulysse commented Feb 12, 2024

@nf-core-bot fix linting pretty please

@maxulysse maxulysse merged commit dc05d53 into nf-core:dev Feb 12, 2024
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