v2.2 - Lead Liger

Template

• Update repo logos to utilize GitHub's #gh-light/dark-mode-only, to switch between logos optimized for light or dark themes. The old repo logos have to be removed (in docs/images and assets/).
• Deal with authentication with private repositories
• Bump minimun Nextflow version to 21.10.3
• Convert pipeline template to updated Nextflow DSL2 syntax
• Solve circular import when importing nf_core.modules.lint
• Disable cache in nf_core.utils.fetch_wf_config while performing test_wf_use_local_configs.
• Modify software version channel handling to support multiple software version emissions (e.g. from mulled containers), and multiple software versions.
• Update dumpsoftwareversion module to correctly report versions with trailing zeros.
• Remove params.hostnames from the pipeline template (#1304)
• Update .gitattributes to mark installed modules and subworkflows as linguist-generated (#1311)
• Adding support for Julia package environments to nextflow.config(#1317)
• New YAML issue templates for pipeline bug reports and feature requests, with a much richer interface (#1165)
• Update AWS test GitHub Actions to use v2 of nf-core/tower-action
• Post linting comment even when linting.yml fails
• Update CONTRIBUTION.md bullets to remove points related to scrape_software_versions.py
• Update AWS test to set Nextflow version to 21.10.3

General

• Made lint check for parameters defaults stricter [#992]
  • Default values in nextflow.config must match the defaults given in the schema (anything with { in, or in main.nf is ignored)
  • Defaults in nextflow.config must now match the variable type specified in the schema
  • If you want the parameter to not have a default value, use null
  • Strings set to false or an empty string in nextflow.config will now fail linting
• Bump minimun Nextflow version to 21.10.3
• Changed questionary ask() to unsafe_ask() to not catch KeyboardInterupts (#1237)
• Fixed bug in nf-core launch due to revisions specified with -r not being added to nextflow command. (#1246)
• Update regex in readme test of nf-core lint to agree with the pipeline template (#1260)
• Update 'fix' message in nf-core lint to conform to the current command line options. (#1259)
• Fixed bug in nf-core list when NXF_HOME is set
• Run CI test used to create and lint/run the pipeline template with minimum and latest edge release of NF (#1304)
• New YAML issue templates for tools bug reports and feature requests, with a much richer interface (#1165)
• Handle synax errors in Nextflow config nicely when running nf-core schema build (#1267)
• Erase temporary files and folders while performing Python tests (pytest)
• Remove base Dockerfile used for DSL1 pipeline container builds
• Run tests with Python 3.10
• #1363 Fix tools CI workflow nextflow versions.

Modules

• Fixed typo in module_utils.py.
• Fixed failing lint test when process section was missing from module. Also added the local failing tests to the warned section of the output table. (#1235)
• Added --diff flag to nf-core modules update which shows the diff between the installed files and the versions
• Update nf-core modules create help texts which were not changed with the introduction of the --dir flag
• Check if README is from modules repo
• Update module template to DSL2 v2.0 (remove functions.nf from modules template and updating main.nf (#1289)
• Substitute get process/module name custom functions in module main.nf using template replacement (#1284)
• Linting now fails instead of warning if a local copy of a module does not match the remote (#1313)
• Check test YML file for md5sums corresponding to empty files (#1302)
• Exit with an error if empty files are found when generating the test YAML file (#1302)