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Update all modules to have environment name #1327

Merged
merged 7 commits into from
Nov 15, 2023
Merged

Update all modules to have environment name #1327

merged 7 commits into from
Nov 15, 2023

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FriederikeHanssen
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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/sarek 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 Nov 14, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit 24eafe0

+| ✅ 143 tests passed       |+
#| ❔   9 tests were ignored |#
!| ❗   5 tests had warnings |!

❗ Test warnings:

  • nextflow_config - Config manifest.version should end in dev: 3.4.0
  • pipeline_todos - TODO string in WorkflowSarek.groovy: Optionally add in-text citation tools to this list.
  • schema_description - No description provided in schema for parameter: bcftools_annotations
  • schema_description - No description provided in schema for parameter: bcftools_annotations_index
  • schema_description - No description provided in schema for parameter: bcftools_header_lines

❔ Tests ignored:

  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: assets/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_light.png
  • files_unchanged - File ignored due to lint config: docs/images/nf-core-sarek_logo_dark.png
  • files_unchanged - File ignored due to lint config: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • template_strings - template_strings

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-11-14 21:32:33

maxulysse
maxulysse reviewed Nov 14, 2023
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@maxulysse
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cf nf-core/modules#4332

@maxulysse
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Freebayes is a bit unstable, usually a restart does it for the tests, but it's unreliable.
Remember to add untar to the exclude matrix
And sorry, but since we have updated sentieon files, all the sentieon tests are failing

@asp8200
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asp8200 commented Nov 14, 2023

Freebayes is a bit unstable, usually a restart does it for the tests, but it's unreliable. Remember to add untar to the exclude matrix And sorry, but since we have updated sentieon files, all the sentieon tests are failing

The sentieon-tests always fails on PR's coming from "outside nf-core", and I think that is what we are seeing here:

 Unknown config secret 'SENTIEON_AUTH_MECH_BASE64' -- Check script './workflows/../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_sentieon_haplotyper/../../../modules/nf-core/sentieon/haplotyper/main.nf' at line: 40

@maxulysse
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Freebayes is a bit unstable, usually a restart does it for the tests, but it's unreliable. Remember to add untar to the exclude matrix And sorry, but since we have updated sentieon files, all the sentieon tests are failing

The sentieon-tests always fails on PR's coming from "outside nf-core", and I think that is what we are seeing here:

 Unknown config secret 'SENTIEON_AUTH_MECH_BASE64' -- Check script './workflows/../subworkflows/local/bam_variant_calling_germline_all/../bam_variant_calling_sentieon_haplotyper/../../../modules/nf-core/sentieon/haplotyper/main.nf' at line: 40

yeah, that's why I was not worried about them

@FriederikeHanssen
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yeeah will ignore the sentieon tests here. There are no crucial changes and they will be run again the moment we merge to dev

edmundmiller
edmundmiller approved these changes Nov 14, 2023
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Looks good to me! I need to wrap up the scatter stuff and bring it in here...

@FriederikeHanssen FriederikeHanssen merged commit ca7be8d into nf-core:dev Nov 15, 2023
86 of 103 checks passed
@FriederikeHanssen FriederikeHanssen deleted the conda_env_name branch November 15, 2023 08:15
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@edmundmiller edmundmiller edmundmiller approved these changes

@maxulysse maxulysse maxulysse approved these changes

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@FriederikeHanssen @maxulysse @asp8200 @edmundmiller