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Update Mirbase URLs structure to match their new structure #269

Merged
merged 1 commit into from Sep 1, 2023
Merged

Update Mirbase URLs structure to match their new structure #269

merged 1 commit into from Sep 1, 2023

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robsyme
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@robsyme robsyme commented Aug 23, 2023

Mirbase has changed where they host genoms, hairpin and mature fasta files.

Previously: https://mirbase.org/ftp/CURRENT/mature.fa.gz
Updated: https://mirbase.org/download/CURRENT/mature.fa

Note that Mirbase no longer hosts the compressed version of these files - only the uncompressed fa version.

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/smrnaseq 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).

@robsyme
Mirbase has changed their URL structure, so we need to update the URLs
7ea85c4 
in the configuration files and docs.

Signed-off-by: Rob Syme <rob.syme@gmail.com>
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github-actions bot commented Aug 23, 2023 •
edited

nf-core lint overall result: Failed ❌

Posted for pipeline commit 7ea85c4

+| ✅ 148 tests passed       |+
!| ❗   3 tests had warnings |!
-| ❌   8 tests failed       |-

❌ Test failures:

  • nextflow_config - Config variable not found: params.validationShowHiddenParams
  • nextflow_config - Config variable not found: params.validationSchemaIgnoreParams
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml does not match the template
  • files_unchanged - assets/nf-core-smrnaseq_logo_light.png does not match the template
  • files_unchanged - lib/NfcoreTemplate.groovy does not match the template
  • schema_params - Param schema_ignore_params from nextflow config not found in nextflow_schema.json
  • multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 2.2.2
  • 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

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-23 17:09:09

@apeltzer apeltzer mentioned this pull request Aug 30, 2023
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@apeltzer apeltzer added this to the 2.2.1 milestone Aug 30, 2023
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Will now work on #260 to get template updates in, so this can be merged for a new patch release 👍🏻

This was referenced Aug 30, 2023
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@apeltzer apeltzer changed the base branch from dev to merge-template-2.9 September 1, 2023 11:34
@apeltzer apeltzer merged commit 9c09116 into nf-core:merge-template-2.9 Sep 1, 2023
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