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Nf test bbmap bbsplit #1094

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wants to merge 19 commits into from
Closed

Nf test bbmap bbsplit #1094

wants to merge 19 commits into from

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Joon-Klaps
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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/rnaseq 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).

maxulysse and others added 19 commits June 14, 2023 13:15
@maxulysse
Update public_aws_ecr.config
b94d105
@MatthiasZepper
Display a warning when '--star_extra_alignment_args' are used in comb…
2e936fd 
…ination with the STAR-RSEM route.
@MatthiasZepper @drpatelh
Apply suggestions from code review
dff30b5 
Co-authored-by: Harshil Patel <[email protected]>
@drpatelh
Merge pull request #1049 from MatthiasZepper/ExtraStarAlignArgsWarning
6636fcc 
Display a warning when '--star_extra_alignment_args' are used with RSEM
@drpatelh
Merge pull request #1048 from nf-core/maxulysse-patch-1
9238ad2 
Update public_aws_ecr.config
@adamrtalbot
Remove public_aws_ecr profile
8261c4e
@adamrtalbot
CHANGELOG
844893e
@drpatelh
Merge pull request #1051 from adamrtalbot/remove_public_aws_ecr_profile
6015eef 
Remove public_aws_ecr profile
@sateeshperi
implement-hisat2-salmon-starrsem-starsalmon-tests-snapshots
4a137b3
@sateeshperi
update-ci-for-nf-test
521e34f
@sateeshperi
update-snapshots-after-module-bumps
4a5fff6
@sateeshperi
update-snapshots-rm-nxf-ver
5aebfe2
@sateeshperi
CI-add-dev-master-pr-comment-test-tap-results
eac9fcd
@sateeshperi
CI-fix-comment-pr-action-forpull-request
ca9e778
@sateeshperi
add-UTILS-lib-update-snapshots
9f03e12
@sateeshperi
rm-docker-hardcode-nf-test-config-add-pipeline-tag
72838d3
@sateeshperi
add-salmon-skip-pseudoalignment-test-update-snapshots
3419e02
@sateeshperi
update snaps after rebase; update UTILS function
537de07
@sateeshperi
update test tags
31a9d62
@github-actions
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This PR is against the master branch ❌

  • Do not close this PR
  • Click Edit and change the base to dev
  • This CI test will remain failed until you push a new commit

Hi @Joon-Klaps,

It looks like this pull-request is has been made against the nf-core/rnaseq master branch.
The master branch on nf-core repositories should always contain code from the latest release.
Because of this, PRs to master are only allowed if they come from the nf-core/rnaseq dev branch.

You do not need to close this PR, you can change the target branch to dev by clicking the "Edit" button at the top of this page.
Note that even after this, the test will continue to show as failing until you push a new commit.

Thanks again for your contribution!

@github-actions
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github-actions bot commented Oct 16, 2023 •
edited
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nf-core lint overall result: Failed ❌

Posted for pipeline commit 31a9d62

+| ✅ 137 tests passed       |+
#| ❔   6 tests were ignored |#
!| ❗   4 tests had warnings |!
-| ❌   9 tests failed       |-

❌ Test failures:

  • nextflow_config - Config variable not found: params.validationShowHiddenParams
  • nextflow_config - Config variable not found: params.validationSchemaIgnoreParams
  • files_unchanged - CODE_OF_CONDUCT.md does not match the template
  • files_unchanged - .github/CONTRIBUTING.md does not match the template
  • files_unchanged - .github/ISSUE_TEMPLATE/bug_report.yml does not match the template
  • files_unchanged - .github/workflows/linting.yml does not match the template
  • files_unchanged - assets/nf-core-rnaseq_logo_light.png does not match the template
  • schema_params - Param schema_ignore_params from nextflow config not found in nextflow_schema.json
  • multiqc_config - 'assets/multiqc_config.yml' does not contain a matching 'report_comment'.

❗ Test warnings:

  • files_exist - File not found: .github/workflows/awstest.yml
  • files_exist - File not found: .github/workflows/awsfulltest.yml
  • nextflow_config - Config manifest.version should end in dev: 3.12.0
  • 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: .gitattributes
  • 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: lib/NfcoreTemplate.groovy
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/rnaseq/rnaseq/.github/workflows/awstest.yml

✅ Tests passed:

Run details

  • nf-core/tools version 2.10
  • Run at 2023-10-16 09:58:08

@Joon-Klaps Joon-Klaps closed this Oct 16, 2023
@drpatelh drpatelh deleted the nf-test-bbmap-bbsplit branch November 21, 2023 09:46
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6 participants
@Joon-Klaps @maxulysse @MatthiasZepper @drpatelh @adamrtalbot @sateeshperi