v2.0 - Palladium Platypus - [2021-07-13]

⚠️ Major enhancements & breaking changes

This marks the first Nextflow DSL2-centric release of tools which means that some commands won't work in full with DSL1 pipelines anymore. Please use a v1.x version of tools for such pipelines or better yet join us to improve our DSL2 efforts! Here are the most important changes:

• The pipeline template has been completely re-written in DSL2
• A module template has been added to auto-create best-practice DSL2 modules to speed up development
• A whole suite of commands have been added to streamline the creation, installation, removal, linting and version bumping of DSL2 modules either installed within pipelines or the nf-core/modules repo

Template

• Move TODO item of contains: map in a YAML string [#1082]
• Trigger AWS tests via Tower API [#1160]

General

• Fixed a bug in the Docker image build for tools that failed due to an extra hyphen. [#1069]
• Regular release sync fix - this time it was to do with JSON serialisation [#1072]
• Fixed bug in schema validation that ignores upper/lower-case typos in parameters [#1087]
• Bugfix: Download should use path relative to workflow for configs
• Remove lint checks for files related to conda and docker as not needed anymore for DSL2
• Removed params_used lint check because of incompatibility with DSL2
• Addedmodules bump-versions command to README.md
• Update docs for v2.0 release

Modules

• Update comment style of modules functions.nf template file [#1076]
• Changed working directory to temporary directory for nf-core modules create-test-yml [#908]
• Use Biocontainers API instead of quayi.io API for nf-core modules create [#875]
• Update nf-core modules install to handle different versions of modules #1116
• Added nf-core modules bump-versions command to update all versions in the nf-core/modules repository [#1123]
• Updated nf-core modules lint to check whether a git_sha exists in the modules.json file or whether a new version is available [#1114]
• Refactored nf-core modules command into one file per command #1124
• Updated nf-core modules remove to also remove entry in modules.json file (#1115)
• Bugfix: Interactive prompt for nf-core modules install was receiving too few arguments
• Added progress bar to creation of 'modules.json'
• Updated nf-core modules list to show versions of local modules
• Improved exit behavior by replacing sys.exit with exceptions
• Updated nf-core modules remove to remove module entry in modules.json if module directory is missing
• Create extra tempdir as work directory for nf-core modules create-test-yml to avoid adding the temporary files to the test.yml
• Refactored passing of command line arguments to nf-core commands and subcommands (#1139, #1140)
• Check for modules.json for entries of modules that are not actually installed in the pipeline [#1141]
• Added <keywords> argument to nf-core modules list for filtering the listed modules. (#1139
• Added support for a bump-versions configuration file [#1142]
• Fixed nf-core modules create-test-yml so it doesn't break when the output directory is supplied [#1148]
• Updated nf-core modules lint to work with new directory structure [#1159]
• Updated nf-core modules install and modules.json to work with new directory structure (#1159)
• Updated nf-core modules remove to work with new directory structure [#1159]
• Restructured code and removed old table style in nf-core modules list
• Fixed bug causing modules.json creation to loop indefinitly
• Added --all flag to nf-core modules install
• Added remote and local subcommands to nf-core modules list
• Fix bug due to restructuring in modules template
• Added checks for verifying that the remote repository is well formed
• Added checks to ModulesCommand for verifying validity of remote repositories
• Misc. changes to modules install: check that module exist in remote, --all is has --latest by default.

Sync

• Don't set the default value to "null" when a parameter is initialised as null in the config [#1074]

Tests

• Added a test for the version_consistency lint check
• Refactored modules tests into separate files, and removed direct comparisons with number of tests in lint tests (#1158)

Template

• Fixed an issue regarding explicit disabling of unused container engines [#972]
• Removed trailing slash from params.igenomes_base to yield valid s3 paths (previous paths work with Nextflow but not aws cli)
• Added a timestamp to the trace + timetime + report + dag filenames to fix overwrite issue on AWS
• Rewrite the params_summary_log() function to properly ignore unset params and have nicer formatting [#971]
• Fix overly strict --max_time formatting regex in template schema [#973]
• Convert d to day in the cleanParameters function to make Duration objects like 2d pass the validation [#858]
• Added nextflow version to quick start section and adjusted nf-core bump-version [#1032]
• Use latest stable Nextflow version 21.04.0 for CI tests instead of the -edge release

Download

• Fix bug in nf-core download where image names were getting a hyphen in nf-core which was breaking things.
• Extensive new interactive prompts for all command line flags [#1027]
  • It is now recommended to run nf-core download without any cli options and follow prompts (though flags can be used to run non-interactively if you wish)
• New helper code to set $NXF_SINGULARITY_CACHEDIR and add to .bashrc if desired [#1027]

Launch

• Strip values from nf-core launch web response which are False and have no default in the schema [#976]
• Improve API caching code when polling the website, fixes noisy log message when waiting for a response [#1029]
• New interactive prompts for pipeline name [#1027]

Modules

• Added tool_name_underscore to the module template to allow TOOL_SUBTOOL in main.nf [#1011]
• Added --conda-name flag to nf-core modules create command to allow sidestepping questionary [#988]
• Extended nf-core modules lint functionality to check tags in test.yml and to look for a entry in the pytest_software.yml file
• Update modules commands to use new test tag format tool/subtool
• New modules lint test comparing the functions.nf file to the template version
• Modules installed from alternative sources are put in folders based on the name of the source repository

Linting

• Fix bug in nf-core lint config skipping for the nextflow_config test [#1019]
• New -k/--key cli option for nf-core lint to allow you to run only named lint tests, for faster local debugging
• Merge markers lint test - ignore binary files, allow config to ignore specific files [#1040]
• New lint test to check if all defined pipeline parameters are mentioned in main.nf [#1038]
• Added fix to remove warnings about params that get converted from camelCase to camel-case [#1035]
• Added pipeline schema lint checks for missing parameter description and parameters outside of groups [#1017]

General

• Try to fix the fix for the automated sync when we submit too many PRs at once [#970]
• Rewrite how the tools documentation is deployed to the website, to allow multiple versions
• Created new Docker image for the tools cli package - see installation docs for details [#917]
• Ignore permission errors for setting up requests cache directories to allow starting with an invalid or read-only HOME directory

This is a patch release fixing some nasty bugs that crept into the code base for the nf-core helper tools. There are no changes to the nf-core pipeline template, so there should be no automated pipeline synchronisation pull-requests for this release.

New features

• Running tests twice with nf-core modules create-test-yml to catch unreproducible md5 sums [#890]
• nf-core modules create command - if no bioconda package is found, prompt user for a different bioconda package name
• Updated module template main.nf with new test data paths

Bug fixes

• Fix sync error again where the Nextflow edge release needs to be used for some pipelines
• Fix bug with nf-core lint --release (NameError: name 'os' is not defined)
• Added linebreak to linting comment so that markdown header renders on PR comment properly

• Added better logging message if a user doesn't specificy the directory correctly with nf-core modules commands [#942]
• Fixed parameter validation bug caused by JSONObject [#937]
• Fixed template creation error regarding file permissions [#932]
• Split the create-lint-wf tests up into separate steps in GitHub Actions to make the CI results easier to read
• Added automated PR comments to the Markdown, YAML and Python lint CI tests to explain failures (tools and pipeline template)
• Make nf-core lint summary table borders coloured according to overall pass / fail status
• Attempted a fix for the automated sync when we submit too many PRs at once [#911]

Minor patch release to scoop up a small few errors discovered after the release.

• Fixed bug in pipeline linting markdown output that gets posted to PR comments [#914]
• Made text for the PR branch CI check less verbose with a TLDR in bold at the top
• A number of minor tweaks to the new nf-core modules lint code

When we do releases, we sometimes like to go big. This is one of those times.

This is a truly huge release of nf-core/tools with a massive amount of new functionality. Please be sure to read the changelog and updated readme carefully!

Note to developers - please run and push the results of nf-core lint --fix before attempting to merge the automated synchronisation PR. This should reduce the size of the diff and make merging a lot easier.

The template and associated updates in this release is for Nextflow DSL1 pipelines. This is likely to be one of the last releases before we officially switch to DSL2. For those of you already with DSL2 pipelines you may need to treat the automated merge PR very carefully. Ask for help on Slack if in any doubt.

Template

• Major new feature - Validation of pipeline parameters [#426]
  • The addition runs as soon as the pipeline launches and checks the pipeline input parameters two main things:
    • No parameters are supplied that share a name with core Nextflow options (eg. --resume instead of -resume)
    • Supplied parameters validate against the pipeline JSON schema (eg. correct variable types, required values)
  • If either parameter validation fails or the pipeline has errors, a warning is given about any unexpected parameters found which are not described in the pipeline schema.
  • This behaviour can be disabled by using --validate_params false
• Added profiles to support the Charliecloud and Shifter container engines [#824]
  • Note that Charliecloud requires Nextflow version v21.03.0-edge or later.
• Profiles for container engines now explicitly disable all other engines [#867]
• Fixed typo in nf-core-lint CI that prevented the markdown summary from being automatically posted on PRs as a comment.
• Changed default for --input from data/*{1,2}.fastq.gz to null, as this is now validated by the schema as a required value.
• Removed support for --name parameter for custom run names.
  • The same functionality for MultiQC still exists with the core Nextflow -name option.
• Added to template docs about how to identify process name for resource customisation
• The parameters --max_memory and --max_time are now validated against a regular expression [#793]
  • Must be written in the format 123.GB / 456.h with any of the prefixes listed in the Nextflow docs
  • Bare numbers no longer allowed, avoiding people from trying to specify GB and actually specifying bytes.
• Switched from cookiecutter to Jinja2 [#880]
• Finally dropped the wonderful cookiecutter library that was behind the first pipeline template that led to nf-core [#880]
  • Now rendering templates directly using Jinja, which is what cookiecutter was doing anyway

Modules

Initial addition of a number of new helper commands for working with DSL2 modules:

• modules list - List available modules
• modules install - Install a module from nf-core/modules
• modules remove - Remove a module from a pipeline
• modules create - Create a module from the template
• modules create-test-yml - Create the test.yml file for a module with md5 sums, tags, commands and names added
• modules lint - Check a module against nf-core guidelines

You can read more about each of these commands in the main tools documentation (see README.md or https://nf-co.re/tools)

Tools helper code

• Fixed some bugs in the command line interface for nf-core launch and improved formatting [#829]
• New functionality for nf-core download to make it compatible with DSL2 pipelines [#832]
  • Singularity images in module files are now discovered and fetched
  • Direct downloads of Singularity images in python allowed (much faster than running singularity pull)
  • Downloads now work with $NXF_SINGULARITY_CACHEDIR so that pipelines sharing containers have efficient downloads
• Changed behaviour of nf-core sync command [#787]
  • Instead of opening or updating a PR from TEMPLATE directly to dev, a new branch is now created from TEMPLATE and a PR opened from this to dev.
  • This is to make it easier to fix merge conflicts without accidentally bringing the entire pipeline history back into the TEMPLATE branch (which makes subsequent sync merges much more difficult)

Linting

• Major refactor and rewrite of pipieline linting code
  • Much better code organisation and maintainability
  • New automatically generated documentation using Sphinx
  • Numerous new tests and functions, removal of some unnecessary tests
• Added lint check for merge markers [#321]
• Added new option --fix to automatically correct some problems detected by linting
• Added validation of default params to nf-core schema lint [#823]
• Added schema validation of GitHub action workflows to lint function [#795]
• Fixed bug in schema title and description validation
• Added second progress bar for conda dependencies lint check, as it can be slow [#299]
• Added new lint test to check files that should be unchanged from the pipeline.
• Added the possibility to ignore lint tests using a nf-core-lint.yml config file [#809]

Minor release, primarily to fix a problem introduced in v1.12 where not all instances of baseDir had been switched with projectDir. However, the elves have been busy and managed to squeeze in a few extra goodies along with the fix:

Template

• Finished switch from $baseDir to $projectDir in iGenomes.conf and main.nf
  • Main fix is for smail_fields which was a bug introduced in the previous release. Sorry about that!
• Ported a number of small content tweaks from nf-core/eager to the template [#786]
  • Better contributing documentation, more placeholders in documentation files, more relaxed markdownlint exceptions for certain HTML tags, more content for the PR and issue templates.

Tools helper code

• Pipeline schema: make parameters of type range to number. [#738]
• Respect $NXF_HOME when looking for pipelines with nf-core list [#798]
• Swapped PyInquirer with questionary for command line questions in launch.py [#726]
  • This should fix conda installation issues that some people had been hitting
  • The change also allows other improvements to the UI
• Fix linting crash when a file deleted but not yet staged in git [#796]

A bit of a fast cycle on this release, it is needed urgently because GitHub Actions CI tests will be failing on all pipelines due to the set-env and add-path commands being depreciated (see the GitHub blog post for details).

Tools helper code

• Updated nf_core documentation generator for building https://nf-co.re/tools-docs/

Template

• Make CI comments work with PRs from forks [#765]
  • Branch protection and linting results should now show on all PRs
• Updated GitHub issue templates, which had stopped working
• Refactored GitHub Actions so that the AWS full-scale tests are triggered after docker build is finished
  • DockerHub push workflow split into two - one for dev, one for releases
• Updated actions to no longer use set-env which is now depreciating [#739]
• Added config import for test_full in nextflow.config
• Switched depreciated $baseDir to $projectDir
• Updated minimum Nextflow version to 20.04.10
• Make Nextflow installation less verbose in GitHub Actions [#780]

Linting

• Updated code to display colours in GitHub Actions log output
• Allow tests to pass with dev version of nf-core/tools (previous failure due to base image version)
• Lint code no longer tries to post GitHub PR comments. This is now done in a GitHub Action only.

Template

• Fix command error in awstest.yml GitHub Action workflow.
• Allow manual triggering of AWS test GitHub Action workflows.
• Remove TODO item, which was proposing the usage of additional files beside usage.md and output.md for documentation.
• Added a Podman profile, which enables Podman as container.
• Updated linting for GitHub actions AWS tests workflows.

Linting

• Made a base-level Dockerfile a warning instead of failure
• Added a lint failure if the old bin/markdown_to_html.r script is found
• Update rich package dependency and use new markup escaping to change [[!]] back to [!] again

Other

• Pipeline sync - fetch full repo when checking out before sync
• Sync - Add GitHub actions manual trigger option

Second patch release to address some small errors discovered in the pipeline template.
Apologies for the inconvenience.

• Fix syntax error in /push_dockerhub.yml GitHub Action workflow
• Change params.readPaths -> params.input_paths in test_full.config
• Check results when posting the lint results as a GitHub comment
  • This feature is unfortunately not possible when making PRs from forks outside of the nf-core organisation for now.
• More major refactoring of the automated pipeline sync
  • New GitHub Actions matrix parallelisation of sync jobs across pipelines [#673]
  • Removed the --all behaviour from nf-core sync as we no longer need it
  • Sync now uses a new list of pipelines on the website which does not include archived pipelines [#712]
  • When making a PR it checks if a PR already exists - if so it updates it [#710]
  • More tests and code refactoring for more stable code. Hopefully fixes 404 error [#711]