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Update nf #4

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@srbija812 srbija812 added the bug Something isn't working label May 8, 2023
@srbija812 srbija812 requested a review from MillironX May 8, 2023 18:55
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github-actions bot commented May 8, 2023

This PR is against the master branch ❌

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

Hi @srbija812,

It looks like this pull-request is has been made against the ksumngs/v-met 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 ksumngs/v-met dev branch.

You do not need to close this PR, you can change the target branch to develop 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!

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github-actions bot commented May 8, 2023

nf-core lint overall result: Failed ❌

Posted for pipeline commit 5e51f2a

+| ✅  94 tests passed       |+
#| ❔  45 tests were ignored |#
!| ❗   6 tests had warnings |!
-| ❌   5 tests failed       |-

❌ Test failures:

  • nextflow_config - Config variable (incorrectly) found: params.enable_conda
  • nextflow_config - Config manifest.name did not begin with nf-core/:
    ksumngs/v-met
  • nextflow_config - Config variable manifest.homePage did not begin with https://github.com/nf-core/:
    https://ksumngs.github.io/v-met
  • nextflow_config - Config dag.file did not end with .html
  • nextflow_config - Lines for loading custom profiles not found. File should contain: ```groovy
    // Load nf-core custom profiles from different Institutions
    try {
    includeConfig "${params.custom_config_base}/nfcore_custom.config"
    } catch (Exception e) {
    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
    }

❗ Test warnings:

  • files_exist - File not found: assets/multiqc_config.yml
  • files_exist - File not found: pyproject.toml
  • nextflow_config - Config manifest.version should end in dev: '1.0.1'
  • readme - README did not have a Nextflow minimum version badge.
  • pipeline_name_conventions - Naming does not adhere to nf-core conventions: Contains non alphanumeric characters
  • schema_lint - Input mimetype is missing or empty

❔ Tests ignored:

  • files_exist - File is ignored: .markdownlint.yml
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_exist - File is ignored: .github/ISSUE_TEMPLATE/feature_request.yml
  • files_exist - File is ignored: assets/nf-core-v-met_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-v-met_logo_light.png
  • files_exist - File is ignored: docs/images/nf-core-v-met_logo_dark.png
  • files_exist - File is ignored: conf/test_full.config
  • files_exist - File is ignored: docs/output.md
  • files_exist - File is ignored: docs/README.md
  • files_exist - File is ignored: docs/usage.md
  • files_exist - File is ignored: lib/nfcore_external_java_deps.jar
  • files_exist - File is ignored: lib/NfcoreSchema.groovy
  • files_exist - File is ignored: lib/NfcoreTemplate.groovy
  • files_exist - File is ignored: lib/Utils.groovy
  • files_exist - File is ignored: lib/WorkflowMain.groovy
  • files_exist - File is ignored: lib/WorkflowV-met.groovy
  • files_exist - File is ignored: conf/igenomes.config
  • files_exist - File is ignored: .github/workflows/awstest.yml
  • files_exist - File is ignored: .github/workflows/awsfulltest.yml
  • files_unchanged - File ignored due to lint config: .gitattributes
  • files_unchanged - File ignored due to lint config: CODE_OF_CONDUCT.md
  • 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 does not exist: .github/ISSUE_TEMPLATE/bug_report.yml
  • files_unchanged - File ignored due to lint config: .github/ISSUE_TEMPLATE/config.yml
  • files_unchanged - File does not exist: .github/ISSUE_TEMPLATE/feature_request.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: .github/workflows/linting_comment.yml
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.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-v-met_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-v-met_logo_light.png
  • files_unchanged - File does not exist: docs/images/nf-core-v-met_logo_dark.png
  • files_unchanged - File does not exist: docs/README.md
  • files_unchanged - File does not exist: lib/nfcore_external_java_deps.jar
  • files_unchanged - File does not exist: lib/NfcoreSchema.groovy
  • files_unchanged - File does not exist: lib/NfcoreTemplate.groovy
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml
  • actions_ci - actions_ci
  • actions_awstest - 'awstest.yml' workflow not found: /home/runner/work/v-met/v-met/.github/workflows/awstest.yml
  • template_strings - template_strings
  • multiqc_config - 'assets/multiqc_config.yml' not found

✅ Tests passed:

Run details

  • nf-core/tools version 2.8
  • Run at 2023-05-08 19:00:02

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@MillironX MillironX Awaiting requested review from MillironX

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@MillironX MillironX

@ksumolecularngs ksumolecularngs

@srbija812 srbija812

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@srbija812 @MillironX @ksumolecularngs