nf-core/tools: v2.3 - Mercury Vulture

Another big release that's been coming for quite some time (apologies to all who have been running with dev for weeks / months).

One or two major bugfixes, such as making nf-core download work again with the latest DSL2 formats. See below for the full list of changes in this release.

Full Changelog: https://github.com/nf-core/tools/compare/2.2...2.3

• Removed mention of --singularity_pull_docker_container in pipeline README.md
• Replaced equals with ~ in nf-core headers, to stop false positive unresolved conflict errors when committing with VSCode.
• Add retry strategy for AWS megatests after releasing nf-core/tower-action v2.2
• Added .nf-core.yml file with repository_type: pipeline for modules commands
• Update igenomes path to the BWAIndex to fetch the whole version0.6.0 folder instead of only the genome.fa file
• Remove pinned Node version in the GitHub Actions workflows, to fix errors with markdownlint
• Bumped nf-core/tower-action to v3 and removed pipeline and revision from the AWS workflows, which were not needed
• Add yamllint GitHub Action.
• Add .yamllint.yml to avoid line length and document start errors (#1407)
• Add --publish_dir_mode back into the pipeline template (nf-core/rnaseq#752)
• Add optional loading of of pipeline-specific institutional configs to nextflow.config
• Make --outdir a mandatory parameter (nf-core/tools#1415)

• Updated nf-core download to work with latest DSL2 syntax for containers (#1379)
• Made nf-core modules create detect repository type with explicit .nf-core.yml instead of random readme stuff (#1391)
• Added a Gitpod environment and Dockerfile (#1384)
  • Adds conda, Nextflow, nf-core, pytest-workflow, mamba, and pip to base Gitpod Docker image.
  • Adds GH action to build and push Gitpod Docker image.
  • Adds Gitpod environment to template.
  • Adds Gitpod environment to tools with auto build of nf-core tool.
• Shiny new command-line help formatting (#1403)
• Call the command line help with -h as well as --help (was formerly just the latter) (#1404)
• Add .yamllint.yml config file to avoid line length and document start errors in the tools repo itself.
• Switch to yamllint-github-actionto be able to configure yaml lint exceptions (#1404)
• Prevent module linting KeyError edge case (#1321)
• Bump-versions: Don't trim the trailing newline on files, causes editorconfig linting to fail (#1265)
• Handle exception in nf-core list when a broken git repo is found (#1273)
• Updated URL for pipeline lint test docs (#1348)
• Updated nf-core create to tolerate failures and retry when fetching pipeline logos from the website (#1369)

• New command nf-core modules info that prints nice documentation about a module to the terminal :sparkles: (#1427)
• Linting a pipeline now fails instead of warning if a local copy of a module does not match the remote (#1313)
• Fixed linting bugs where warning was incorrectly generated for:
  • Module does not emit software version
  • Container versions do not match
  • input: / output: not being specified in module
  • Allow for containers from other biocontainers resource as defined here
• Fixed traceback when using stageAs syntax as defined here
• Added nf-core schema docs command to output pipline parameter documentation in Markdown format for inclusion in GitHub and other documentation systems (#741)
• Allow conditional process execution from the configuration file (#1393)
• Add linting for when condition(#1397)
• Added modules ignored table to nf-core modules bump-versions. (#1234)
• Added --conda-package-version flag for specifying version of conda package in nf-core modules create. (#1238)
• Add option of writing diffs to file in nf-core modules update using either interactive prompts or the new --diff-file flag.
• Fixed edge case where module names that were substrings of other modules caused both to be installed (#1380)
• Tweak handling of empty files when generating the test YAML (#1376)
  • Fail linting if a md5sum for an empty file is found (instead of a warning)
  • Don't skip the md5 when generating a test file if an empty file is found (so that linting fails and can be manually checked)
• Linting checks test files for TODO statements as well as the main module code (#1271)
• Handle error if manifest isn't set in nextflow.config (#1418)