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fix: default metadata fields for ENA API v2.0 #148

Merged
merged 9 commits into from
May 3, 2023
Merged

fix: default metadata fields for ENA API v2.0 #148

merged 9 commits into from
May 3, 2023

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ejseqera
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@ejseqera ejseqera commented May 3, 2023

ENA API was just updated as of 05/02/2023. Portal API spec for v2.0 has changed and is breaking the pipeline currently. This PR updates the default metadata fields fetched from ENA to match the new spec and updates the fields used to create id_mappings.csv.

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/fetchngs 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).

drpatelh and others added 9 commits November 9, 2021 15:26
@ejseqera ejseqera added the bug Something isn't working label May 3, 2023
@ejseqera ejseqera requested review from robsyme and maxulysse May 3, 2023 02:32
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github-actions bot commented May 3, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 9e454f2

+| ✅ 153 tests passed       |+
#| ❔   2 tests were ignored |#
!| ❗   3 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: lib/WorkflowFetchngs.groovy
  • 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: assets/sendmail_template.txt
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy

✅ Tests passed:

Run details

  • nf-core/tools version 2.7.2
  • Run at 2023-05-03 02:34:07

robsyme
robsyme reviewed May 3, 2023
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bin/sra_ids_to_runinfo.py
"run_accession",
"experiment_accession",
"sample_accession",
"secondary_sample_accession",
"study_accession",
"secondary_study_accession",
"parent_study",
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Rather than removing parent_study, might it be sensible to use the renamed version of this field, parent_study_accession?

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@ejseqera ejseqera May 3, 2023 •
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parent_study_accession is not a valid field in the run metadata available. This will throw an error so I've omitted it entirely. There does not seem to be a similar renamed field available.

bin/sra_ids_to_runinfo.py
@@ -84,7 +82,6 @@
"sample_title",
"experiment_title",
"study_title",
"description",
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The description field is not among the list of changed fields in the ENA Portal API changes document that you linked. Is this an unannounced change?

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Seems like it. I believe this was replaced with sample_description exclusively.

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robsyme commented May 3, 2023

Great work Esha, thanks!

@ejseqera ejseqera merged commit f6a0d61 into nf-core:dev May 3, 2023
@ejseqera ejseqera deleted the fixena branch May 3, 2023 19:43
@drpatelh drpatelh mentioned this pull request May 6, 2023
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@maxulysse maxulysse maxulysse approved these changes

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@ejseqera @robsyme @maxulysse @drpatelh @Midnighter