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Bump nf-core from 2.1 to 2.6#60

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Bump nf-core from 2.1 to 2.6#60
dependabot[bot] wants to merge 1 commit intomasterfrom
dependabot/pip/nf-core-2.6

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@dependabot dependabot bot commented on behalf of github Oct 5, 2022

Bumps nf-core from 2.1 to 2.6.

Release notes

Sourced from nf-core's releases.

v2.6 - Tin Octopus


⚠️ Please read

This release goes together with a major update on nf-core/modules that restructures DSL2 module files and updates the syntax of modules.json.

These changes have been brought about to accommodate the imminent release of shared subworkflows.

Please be aware of some points:

  • ♻️ You will need to run nf-core modules update on your pipeline which should move a lot of files around
  • 💀 Any module .patch files from nf-core modules patch may be lost (if you have any). Please take care to regenerate them.

If you have any issues, please drop us a line on Slack on the #tools channel 👍🏻


Template

  • Add actions/upload-artifact step to the awstest workflows, to expose the debug log file
  • Add prettier as a requirement to Gitpod Dockerimage
  • Bioconda incompatible conda channel setups now result in more informative error messages (#1812)
  • Update MultiQC module, update supplying MultiQC default and custom config and logo files to module
  • Add a 'recommend' methods description text to MultiQC to help pipeline users report pipeline usage in publications (#1749)
  • Fix template spacing modified by JINJA (#1830)
  • Fix MultiQC execution on template #1855
  • Don't skip including base.config when skipping nf-core/configs

Linting

  • Pipelines: Check that the old renamed lib files are not still present:
    • Checks.groovy -> Utils.groovy
    • Completion.groovy -> NfcoreTemplate.groovy
    • Workflow.groovy -> WorkflowMain.groovy

General

  • Add function to enable chat notifications on MS Teams, accompanied by hook_url param to enable it.
  • Schema: Remove allOf if no definition groups are left.
  • Use contextlib to temporarily change working directories (#1819)
  • More helpful error messages if nf-core download can't parse a singularity image download

Modules

  • If something is wrong with the local repo cache, offer to delete it and try again (#1850)
  • Restructure code to work with the directory restructuring in modules (#1859)
  • Make label: process_single default when creating a new module

... (truncated)

Changelog

Sourced from nf-core's changelog.

v2.6 - Tin Octopus - [2022-10-04]

Template

  • Add actions/upload-artifact step to the awstest workflows, to expose the debug log file
  • Add prettier as a requirement to Gitpod Dockerimage
  • Bioconda incompatible conda channel setups now result in more informative error messages (#1812)
  • Update MultiQC module, update supplying MultiQC default and custom config and logo files to module
  • Add a 'recommend' methods description text to MultiQC to help pipeline users report pipeline usage in publications (#1749)
  • Fix template spacing modified by JINJA (#1830)
  • Fix MultiQC execution on template #1855
  • Don't skip including base.config when skipping nf-core/configs

Linting

  • Pipelines: Check that the old renamed lib files are not still present:
    • Checks.groovy -> Utils.groovy
    • Completion.groovy -> NfcoreTemplate.groovy
    • Workflow.groovy -> WorkflowMain.groovy

General

  • Add function to enable chat notifications on MS Teams, accompanied by hook_url param to enable it.
  • Schema: Remove allOf if no definition groups are left.
  • Use contextlib to temporarily change working directories (#1819)
  • More helpful error messages if nf-core download can't parse a singularity image download

Modules

  • If something is wrong with the local repo cache, offer to delete it and try again (#1850)
  • Restructure code to work with the directory restructuring in modules (#1859)
  • Make label: process_single default when creating a new module

v2.5.1 - Gold Otter Patch - [2022-08-31]

  • Patch release to fix black linting in pipelines (#1789)
  • Add isort options to pyproject.toml (#1792)
  • Lint pyproject.toml file exists and content (#1795)
  • Update GitHub PyPI package release action to v1 (#1785)

v2.5 - Gold Otter - [2022-08-30]

Template

  • Bumped Python version to 3.7 in the GitHub linting in the workflow template (#1680)
  • Fix bug in pipeline readme logo URL (#1590)
  • Switch CI to use setup-nextflow action to install Nextflow (#1650)
  • Add CITATION.cff #361
  • Add Gitpod and Mamba profiles to the pipeline template (#1673)
  • Remove call to getGenomeAttribute in main.nf when running nf-core create without iGenomes (#1670)

... (truncated)

Commits
  • dec66ab Merge pull request #1872 from nf-core/new-screenshots
  • 1a5fb43 Generate new screengrabs with rich-codex
  • d2f9ce7 Merge pull request #1871 from nf-core/dev
  • 3a5cbc5 Merge pull request #1870 from mirpedrol/fix
  • e37f6ab try to find module sha with the old repo path structure
  • 3e95d3b Merge pull request #1869 from ewels/lint-progress-bar
  • 4d7c8ad Fix isort
  • 6c5d065 Merge pull request #1867 from mirpedrol/reinstall
  • 7ca39d8 Add env variable HIDE_PROGRESS to hide progress bars
  • 0d23e9a Merge pull request #1861 from nf-core/dev
  • Additional commits viewable in compare view

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Bumps [nf-core](https://github.com/nf-core/tools) from 2.1 to 2.6.
- [Release notes](https://github.com/nf-core/tools/releases)
- [Changelog](https://github.com/nf-core/tools/blob/master/CHANGELOG.md)
- [Commits](nf-core/tools@2.1...2.6)

---
updated-dependencies:
- dependency-name: nf-core
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
@dependabot dependabot bot added dependencies Pull requests that update a dependency file python Pull requests that update Python code labels Oct 5, 2022
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dependabot bot commented on behalf of github Dec 9, 2022

Superseded by #64.

@dependabot dependabot bot closed this Dec 9, 2022
@dependabot dependabot bot deleted the dependabot/pip/nf-core-2.6 branch December 9, 2022 04:08
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