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Fix samplesheet path from s3 to GH#434

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jfy133 merged 2 commits intodevfrom
fix-samplesheet-path
May 8, 2023
Merged

Fix samplesheet path from s3 to GH#434
jfy133 merged 2 commits intodevfrom
fix-samplesheet-path

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@jfy133 jfy133 commented May 8, 2023

closes #415

Uses updated samplesheet with correct locations of data on s3 (now iGenomes), and the updated samplesheet location now on GitHub nf-core/testdatasets so we can more easily modify this (rather than on s3 bucket where it's not easily modifiable).

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/mag 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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github-actions Bot commented May 8, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 29a3fd8

+| ✅ 158 tests passed       |+
#| ❔   1 tests were ignored |#
!| ❗   1 tests had warnings |!
Details

❗ Test warnings:

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

❔ Tests ignored:

  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-05-08 09:33:17

d4straub
d4straub approved these changes May 8, 2023
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LGTM

@jfy133 jfy133 merged commit 1b2f03c into dev May 8, 2023
@jfy133 jfy133 deleted the fix-samplesheet-path branch June 23, 2023 19:39
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