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Implement ffq #100

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First pass implementation to use ffq to fetch metadata from public databases.

@drpatelh drpatelh changed the title Updates Implement ffq Jun 30, 2022
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github-actions bot commented Jun 30, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 4506619

+| ✅ 143 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   4 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: lib/WorkflowFetchngs.groovy
  • nextflow_config - Config manifest.version should end in dev: '1.7'
  • readme - README did not have a Nextflow minimum version badge.

❔ Tests ignored:

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

✅ Tests passed:

Run details

  • nf-core/tools version 2.4.1
  • Run at 2022-07-01 16:22:50

@drpatelh drpatelh marked this pull request as draft June 30, 2022 20:37
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Tests are expected to fail here due to recent breaking changes introduces in the NCBI API.

The plan is to try and get the tests passing again using ffq instead and to try and maintain feature parity with the existing release in terms of the samplesheet output and id compatibility.

This was referenced Jul 21, 2022
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@adf-ncgr adf-ncgr mentioned this pull request Oct 13, 2022
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