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Fix generation of dict_proteinId_assemblyIds for Entrez download #3

Merged
merged 5 commits into from
Jan 27, 2022
Merged

Fix generation of dict_proteinId_assemblyIds for Entrez download #3

merged 5 commits into from
Jan 27, 2022

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skrakau
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@skrakau skrakau commented Dec 23, 2021 •
edited by AntoniaSchuster
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Fixing bug in bin/download_proteins_entrez.py : dict_proteinId_assemblyIds was buggy since the referenced assemblyIds was unintentionally changed by .append() (causing wrong and not reproducible results in entrez_data/entities_proteins.entrez.tsv). Fixed this by initialising dict_proteinId_assemblyIds with empty sets.

This addresses the issue mentioned by @AntoniaSchuster in qbic-pipelines/metapep#17.

PR checklist

  • This comment contains a description of changes (with reason)
  • CHANGELOG.md is updated
  • If you've fixed a bug or added code that should be tested, add tests!
  • Documentation in docs is updated
  • If necessary, also make a PR on the nf-core/metapep branch on the nf-core/test-datasets repo

@skrakau skrakau mentioned this pull request Dec 23, 2021
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AntoniaSchuster
AntoniaSchuster approved these changes Jan 3, 2022
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Ah that makes sense, looks good now :)

@AntoniaSchuster AntoniaSchuster mentioned this pull request Jan 11, 2022
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github-actions bot commented Jan 26, 2022 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 725cff4

+| ✅ 141 tests passed       |+
!| ❗  12 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • pipeline_todos - TODO string in README.md: Add full-sized test dataset and amend the paragraph below if applicable
  • pipeline_todos - TODO string in README.md: If applicable, make list of people who have also contributed
  • pipeline_todos - TODO string in README.md: Add citation for pipeline after first release. Uncomment lines below and update Zenodo doi and badge at the top of this file.
  • pipeline_todos - TODO string in usage.md: Add documentation about anything specific to running your pipeline. For general topics, please point to (and add to) the main nf-core website.
  • pipeline_todos - TODO string in output.md: Write this documentation describing your workflow's output
  • pipeline_todos - TODO string in test_full.config: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
  • pipeline_todos - TODO string in test_full.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in test.config: Specify the paths to your test data on nf-core/test-datasets
  • pipeline_todos - TODO string in test.config: Give any required params for the test so that command line flags are not needed
  • pipeline_todos - TODO string in WorkflowMain.groovy: Add Zenodo DOI for pipeline after first release
  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

✅ Tests passed:

Run details

  • nf-core/tools version 2.2
  • Run at 2022-01-27 09:06:26

@AntoniaSchuster AntoniaSchuster merged commit cda8103 into nf-core:dev Jan 27, 2022
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@skrakau @AntoniaSchuster