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Added a new feature branch 'copo_metadata' to solve issue #115 #137

Merged
merged 20 commits into from
Sep 11, 2024
Merged

Added a new feature branch 'copo_metadata' to solve issue #115 #137

merged 20 commits into from
Sep 11, 2024

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SandraBabirye
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@SandraBabirye SandraBabirye commented Sep 3, 2024 •
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  • Added a python script that parses the json file that is downloaded from the COPO datasource to extract metadata from it
  • Extracted only relevant information for the genome note from the parsed file
  • Add the list of files in bin/combine_parsed_data.py ie " ("COPO_BIOSAMPLE", "copo_biosample_wgs_file"),
    ("COPO_BIOSAMPLE_HIC", "copo_biosample_hic_file"),
    ("COPO_BIOSAMPLE_RNA", "copo_biosample_rna_file"),"
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).

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github-actions bot commented Sep 3, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit b708ede

+| ✅ 131 tests passed       |+
#| ❔  21 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-genomenote_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomenote_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-genomenote_logo_dark.png
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/config.yml
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/igenomes.config
  • nextflow_config - Config variable ignored: manifest.name
  • nextflow_config - Config variable ignored: manifest.homePage
  • files_unchanged - File ignored due to lint config: LICENSE or LICENSE.md or LICENCE or LICENCE.md
  • files_unchanged - File ignored due to lint config: .github/CONTRIBUTING.md
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File does not exist: assets/nf-core-genomenote_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomenote_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-genomenote_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/genomenote/genomenote/.github/workflows/awstest.yml
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2024-09-11 05:09:47

@BethYates BethYates merged commit 7111172 into sanger-tol:public_dev Sep 11, 2024
6 checks passed
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@SandraBabirye @BethYates