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Fix Input Handling for query_ids in FILTER_QUERY Process #27

Merged
merged 3 commits into from
Sep 23, 2024
Merged

Fix Input Handling for query_ids in FILTER_QUERY Process #27

merged 3 commits into from
Sep 23, 2024

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kylacochrane
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@kylacochrane kylacochrane commented Sep 20, 2024 •
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This PR addresses Issue26.

Problem:
In the FILTER_QUERY process, the input query_ids was originally defined as a val. However, query_ids is now stored as a file, and the process needs to reference the path to the file. This caused an issue where the file was being stored in a temporary directory, leading to file path resolution errors during execution, particularly on Azure.

Solution:
This PR changes the input for query_ids from:

input: val query_ids
TO
input: path query_ids

  • By switching to path, the process can correctly reference the file path and resolve the file during execution.
  • This change improves compatibility across environments, including local, cluster, and cloud setups (Azure).

PR checklist

  • This comment contains a description of changes (with reason).
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Check for unexpected warnings in debug mode (nextflow run . -profile debug,test,docker --outdir <OUTDIR>).
  • CHANGELOG.md is updated.

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github-actions bot commented Sep 20, 2024 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 07a8762

+| ✅ 145 tests passed       |+
#| ❔  22 tests were ignored |#
!| ❗   2 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 0.2.3
  • schema_lint - Schema $id should be https://raw.githubusercontent.com/phac-nml/gasnomenclature/master/nextflow_schema.json
    Found https://raw.githubusercontent.com/phac-nml/gasnomenclature/main/nextflow_schema.json

❔ Tests ignored:

  • files_exist - File is ignored: assets/nf-core-gasnomenclature_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-gasnomenclature_logo_dark.png
  • files_exist - File is ignored: docs/images/nf-core-gasnomenclature_logo_light.png
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • 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 ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/branch.yml
  • files_unchanged - File ignored due to lint config: assets/email_template.html
  • files_unchanged - File ignored due to lint config: assets/email_template.txt
  • files_unchanged - File ignored due to lint config: assets/sendmail_template.txt
  • files_unchanged - File does not exist: assets/nf-core-gasnomenclature_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-gasnomenclature_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-gasnomenclature_logo_dark.png
  • files_unchanged - File ignored due to lint config: docs/README.md
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/gasnomenclature/gasnomenclature/.github/workflows/awstest.yml
  • actions_awsfulltest - actions_awsfulltest
  • pipeline_name_conventions - pipeline_name_conventions

✅ Tests passed:

Run details

  • nf-core/tools version 2.14.1
  • Run at 2024-09-23 18:41:31

@kylacochrane kylacochrane marked this pull request as ready for review September 23, 2024 14:34
apetkau
apetkau approved these changes Sep 23, 2024
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This looks great. Thanks so much for this fix Kyla 😄

CHANGELOG.md
@@ -3,6 +3,13 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## [0.2.3] - 2024/09/20
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Thanks for adding 😄. Could you add the link to this version/tag as well in this file.

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Of course: 07a8762

@kylacochrane kylacochrane merged commit f781232 into dev Sep 23, 2024
4 checks passed
@kylacochrane kylacochrane deleted the fix_filterquery branch September 23, 2024 19:03
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@apetkau apetkau apetkau approved these changes

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@kylacochrane @apetkau