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Adds emit statement for FASTQs and metadata to SRA workflow #184

Merged
merged 3 commits into from
Aug 24, 2023
Merged

Adds emit statement for FASTQs and metadata to SRA workflow #184

merged 3 commits into from
Aug 24, 2023

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@adamrtalbot adamrtalbot commented Aug 21, 2023 •
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Adds emit statement to SRA and SYNAPSE workflow which can be observed and checked in nf-test outputs. Makes the workflows more modular and portable.

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).

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github-actions bot commented Aug 21, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 97af5cd

+| ✅ 135 tests passed       |+
#| ❔  12 tests were ignored |#
!| ❗   7 tests had warnings |!

❗ Test warnings:

  • files_exist - File not found: conf/igenomes.config
  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • files_exist - File not found: lib/WorkflowFetchngs.groovy
  • nextflow_config - Config manifest.version should end in dev: 1.10.1
  • 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
  • schema_description - No description provided in schema for parameter: dbgap_key

❔ Tests ignored:

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-08-24 14:54:57

@adamrtalbot adamrtalbot changed the title Adds emit statement for FASTQs and metadata to SRA workflow [WIP] Adds emit statement for FASTQs and metadata to SRA workflow Aug 21, 2023
@adamrtalbot adamrtalbot force-pushed the emit_statement_to_SRA_workflow branch from c04e042 to 81324d2 Compare August 24, 2023 13:54
@adamrtalbot adamrtalbot changed the title [WIP] Adds emit statement for FASTQs and metadata to SRA workflow Adds emit statement for FASTQs and metadata to SRA workflow Aug 24, 2023
@adamrtalbot adamrtalbot changed the base branch from dev to refactor August 24, 2023 14:52
adamrtalbot
adamrtalbot commented Aug 24, 2023
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CHANGELOG.md Outdated Show resolved Hide resolved
@maxulysse maxulysse merged commit e7c2e18 into nf-core:refactor Aug 24, 2023
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@adamrtalbot @maxulysse