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nf-core/tools: Changelog

v2.10 - Nickel Ostrich + [2023-09-25]

Template

  • Fix links in multiqc_config.yml (#2372 and #2412)
  • Remove default false from nextflow_schema.json (#2376)
  • Add module MULTIQC to modules.config (#2377)
  • Add GitHub workflow for automated release announcements (#2382)
  • Update the Code of Conduct (#2381)
  • Save template information to .nf-core.yml and deprecate argument --template-yaml for nf-core sync (#2388 and #2389)
  • (#2397) Remove fixed Ubuntu test and added to standard testing matrix
  • (#2396) Reduce container finding error to warning since the registries are not consistent.
  • (#2415) Add autoMounts for apptainer.
  • Remove igenomes_base from the schema, so that nf-validation doesn't create a file path and throw errors offline for s3 objects.
  • Modified devcontainer permissions so that singularity can be run in Codespaces/VS Code devcontainers (Commit a103f44)
  • Update Gitpod profile resources to reflect base environment settings.
  • (#747) Add to the template the code to dump the selected pipeline parameters into a json file.

Download

  • Improved container image resolution and prioritization of http downloads over Docker URIs (#2364).
  • Registries provided with -l/--container-library will be ignored for modules with explicit container registry specifications (#2403).
  • Fix unintentional downloading of containers in test for the Tower download functionality. Bug reported by @adamrtalbot and @awgymer (#2434).

Linting

  • Add new command nf-core subworkflows lint (#2379)

Modules

Subworkflows

  • Fix bug: missing subworkflow name when using nf-core subworkflows create (#2435)

General

  • Initialise docker_image_name to fix UnboundLocalError error (#2374)
  • Fix prompt pipeline revision during launch (#2375)
  • Add a create-params-file command to create a YAML parameter file for a pipeline containing parameter documentation and defaults. (#2362)
  • Update the Code of Conduct (#2381)
  • Remove --no-git option from nf-core create (#2394)
  • Throw warning when custom workflow name contains special characters (#2401)
  • Bump version of nf-test snapshot files with nf-core bump-version (#2410)

v2.9 - Chromium Falcon + [2023-06-29]

Template

  • params.max_multiqc_email_size is no longer required (#2273)
  • Remove cleanup = true from test_full.config in pipeline template (#2279)
  • Fix usage docs for specifying params.yaml (#2279)
  • Added stub in modules template (#2277) [Contributed by @nvnieuwk]
  • Move registry definitions out of profile scope ([#2286])(nf-core#2286)
  • Remove aws_tower profile ([#2287])(nf-core#2287)
  • Fixed the Slack report to include the pipeline name (#2291)
  • Fix link in the MultiQC report to point to exact version of output docs (#2298)
  • Updates seqeralabs/action-tower-launch to v2.0.0 (#2301)
  • Remove schema validation from lib folder and use Nextflow nf-validation plugin instead (#1771)
  • Fix parsing of container directive when it is not typical nf-core format (#2306)
  • Add ability to specify custom registry for linting modules, defaults to quay.io (#2313)
  • Add singularity.registry = 'quay.io' in pipeline template (#2305)
  • Add apptainer.registry = 'quay.io' in pipeline template (#2352)
  • Bump minimum required NF version in pipeline template from 22.10.1 -> 23.04.0 (#2305)
  • Add ability to interpret docker.registry from nextflow.config file. If not found defaults to quay.io. (#2318)
  • Add functions to dynamically include pipeline tool citations in MultiQC methods description section for better reporting. (#2326)
  • Remove --tracedir parameter (#2290)
  • Incorrect config parameter warnings when customising pipeline template (#2333)
  • Use markdown syntax in the description for the meta map channels (#2358)

Download

  • Introduce a --tower flag for nf-core download to obtain pipelines in an offline format suited for seqeralabs® Nextflow Tower (#2247).
  • Refactored the CLI for --singularity-cache in nf-core download from a flag to an argument. The prior options were renamed to amend (container images are only saved in the $NXF_SINGULARITY_CACHEDIR) and copy (a copy of the image is saved with the download). remote was newly introduced and allows to provide a table of contents of a remote cache via an additional argument --singularity-cache-index (#2247).
  • Refactored the CLI parameters related to container images. Although downloading other images than those of the Singularity/Apptainer container system is not supported for the time being, a generic name for the parameters seemed preferable. So the new parameter --singularity-cache-index introduced in #2247 has been renamed to --container-cache-index prior to release (#2336).
  • To address issue #2311, a new parameter --container-library was created allowing to specify the container library (registry) from which container images in OCI format (Docker) should be pulled (#2336).
  • Container detection in configs was improved. This allows for DSL2-like container definitions inside the container parameter value provided to process scopes #2346.
  • Add apptainer to the list of false positve container strings (#2353).

Updated CLI parameters

Old parameter New parameter
new parameter -d / --download-configuration
new parameter -t / --tower
-c/ --container -s / --container-system <VALUE>
new parameter -l / --container-library <VALUE>
--singularity-cache -u / --container-cache-utilisation <VALUE>
new parameter -i / --container-cache-index <VALUE>

In addition, -r / --revision has been changed to a parameter that can be provided multiple times so several revisions can be downloaded at once.

Linting

  • Warn if container access is denied (#2270)
  • Error if module container specification has quay.io as prefix when it shouldn't have (#2278
  • Detect if container is 'simple name' and try to contact quay.io server by default (#2281)
  • Warn about null/None/empty default values in nextflow_schema.json (#3328)
  • Fix linting when creating a pipeline skipping some parts of the template and add CI test (#2330)

Modules

  • Don't update modules_json object if a module is not updated (#2323)

Subworkflows

General

  • GitPod base image: Always self-update to the latest version of Nextflow. Add pre-commit dependency.
  • GitPod configs: Update Nextflow as an init task, init pre-commit in pipeline config.
  • Refgenie: Create nxf_home/nf-core/refgenie_genomes.config path if it doesn't exist (#2312)
  • Add CI tests to test running a pipeline whe it's created from a template skipping different areas

v2.8 - Ruthenium Monkey - [2023-04-27]

Template

  • Explicitly disable conda when a container profile (#2140)
  • Turn on automatic clean up of intermediate files in work/ on successful pipeline completion in full-test config (#2163) [Contributed by @jfy133]
  • Add documentation to usage.md on how to use params.yml files, based on nf-core/ampliseq text (#2173) [Contributed by @jfy133, @d4straub]
  • Make jobs automatically resubmit for a much wider range of exit codes (now 104 and 130..145) (#2170)
  • Add a clean-up GHA which closes issues and PRs with specific labels (#2183)
  • Remove problematic sniffer code in samplesheet_check.py that could give false positive 'missing header' errors ([nf-core#2194]) [Contributed by @Midnighter, @jfy133]
  • Consistent syntax for branch checks in PRs (#2202)
  • Fixed minor Jinja2 templating bug that caused the PR template to miss a newline
  • Updated AWS tests to use newly moved seqeralabs/action-tower-launch instead of nf-core/tower-action
  • Remove .cff files from .editorconfig (#2145)
  • Simplify pipeline README (#2186)
  • Added support for the apptainer container engine via -profile apptainer. (#2244) [Contributed by @jfy133]
  • Added config docker.registry to pipeline template for a configurable default container registry when using Docker containers. Defaults to quay.io (#2133)
  • Add tower.yml file to the pipeline template (#2251)
  • Add mastodon badge to README (#2253)
  • Removed quay.io from all module Docker container references as this is now supplied at pipeline level. (#2249)
  • Remove CITATION.cff file from pipeline template, to avoid that pipeline Zenodo entries reference the nf-core publication instead of the pipeline (#2059).

Linting

  • Update modules lint test to fail if enable_conda is found (#2213)
  • Read module lint configuration from .nf-core.yml, not .nf-core-lint.yml (#2221)
  • nf-core schema lint now defaults to linting nextflow_schema.json if no filename is provided (#2225)
  • Warn if /zenodo.XXXXXX is present in the Readme (#2254)
  • Lint all labels in a module (#2227)

Modules

  • Add an --empty-template option to create a module without TODO statements or examples (#2175 & #2177)
  • Removed the nf-core modules mulled command and all its code dependencies (2199).
  • Take into accout the provided --git_remote URL when linting all modules (2243).

Subworkflows

  • Fixing problem when a module included in a subworkflow had a name change from TOOL to TOOL/SUBTOOL (#2177)
  • Fix nf-core subworkflows test not running subworkflow tests (#2181)
  • Add tests for nf-core subworkflows create-test-yml (#2219)

General

  • Deprecate Python 3.7 support because it reaches EOL (#2210)
  • nf-core modules/subworkflows info now prints the include statement for the module/subworkflow (#2182).
  • Add a clean-up GHA which closes issues and PRs with specific labels (#2183)
  • update minimum version of rich to 13.3.1 (#2185)
  • Add the Nextflow version to Gitpod container matching the minimal Nextflow version for nf-core (according to nextflow.config) (#2196)
  • Use nfcore/gitpod:dev container in the dev branch (#2196)
  • Replace requests_mock with responses in test mocks (#2165).
  • Add warning when installing a module from an org_path that exists in multiple remotes in modules.json (#2228 #2239).
  • Add the possibility to translate refgenie asset aliases to the ones used in a pipeline with an alias_translations.yaml file (#2242).
  • Add initial CHM13 support (1988)

v2.7.2 - Mercury Eagle Patch - [2022-12-19]

Template

  • Fix the syntax of github_output in GitHub actions (#2114)
  • Fix a bug introduced in 2.7 that made pipelines hang (#2132)

Linting

  • Allow specifying containers in less than three lines (#2121)
  • Run prettier after dumping a json schema file (#2124)

General

  • Only check that a pipeline name doesn't contain dashes if the name is provided by prompt of --name. Don't check if a template file is used. (#2123)
  • Deprecate --enable_conda parameter. Use conda.enable instead (#2131)
  • Handle json.load() exceptions (#2134)

v2.7.1 - Mercury Eagle Patch - [2022-12-08]

  • Patch release to fix pipeline sync (#2110)

v2.7 - Mercury Eagle - [2022-12-07]

Another big release with lots of new features and bug fixes. Thanks to all contributors!

Highlights

  • New nf-core subworkflows subcommand for creating, removing, testing, updating and finding subworkflows, see the documentation for more information.
  • Every pipeline has now it's own GitHub codespace template, which can be used to develop the pipeline directly in the browser.
  • Improved handling of modules and subworkflows from other repos than nf-core/modules.
  • Pre-commit is now installed as a dependency, which allows us, besides other things, to run prettier on the fly even if it is not manually installed.
  • Shell completion for nf-core commands, more information here.

Template

Features

  • Ignore files in bin/ directory when running prettier (#2080).
  • Add GitHub codespaces template (#1957)
  • nextflow run <pipeline> --version will now print the workflow version from the manifest and exit (#1951).
  • Add profile for running docker with the ARM chips (including Apple silicon) (#1942 and #2034).
  • Flip execution order of parameter summary printing and parameter validation to prevent 'hiding' of parameter errors (#2033).
  • Change colour of 'pipeline completed successfully, but some processes failed' from red to yellow (#2096).

Bug fixes

  • Fix lint warnings for samplesheet_check.nf module (#1875).
  • Check that the workflow name provided with a template doesn't contain dashes (#1822)

Linting

Features

  • Add --sort-by option to linting which allows ordering module lint warnings/errors by either test name or module name (#2077).

Bug fixes

  • Don't lint pipeline name if manifest.name in .nf-core.yml (#2035)
  • Don't check for docker pull commands in actions_ci lint test (leftover from DSL1) (#2055).

General

Features

  • Use pre-commit run prettier if prettier is not available (#1983) and initialize pre-commit in gitpod and codespaces (#1957).
  • Refactor CLI flag --hide-progress to be at the top-level group, like --verbose (#2016)
  • nf-core sync now supports the template YAML file using -t/--template-yaml (#1880).
  • The default branch can now be specified when creating a new pipeline repo #1959.
  • Only warn when checking that the pipeline directory contains a main.nf and a nextflow.config file if the pipeline is not an nf-core pipeline #1964
  • Bump promoted Python version from 3.7 to 3.8 (#1971).
  • Extended the chat notifications to Slack (#1829).
  • Don't print source file + line number on logging messages (except when verbose) (#2015)
  • Automatically format test.yml content with Prettier (#2078)
  • Automatically format modules.json content with Prettier (#2074)
  • Add shell completion for nf-core tools commands(#2070)

Bug fixes, maintenance and tests

  • Fix error in tagging GitPod docker images during releases (#1874).
  • Fix bug when updating modules from old version in old folder structure (#1908).
  • Don't remove local copy of modules repo, only update it with fetch (#1881).
  • Improve test coverage of sync.py and __main__.py (#1936, #1965).
  • Add file versions.yml when generating test.yml with nf-core modules create-test-yml but don't check for md5sum #1963.
  • Mock biocontainers and anaconda api calls in modules and subworkflows tests #1967
  • Run tests with Python 3.11 (#1970).
  • Run test with a realistic version of git (#2043).
  • Fix incorrect file deletion in nf-core launch when --params_in has the same name as --params_out (#1986).
  • Updated GitHub actions (#1998, #2001)
  • Code maintenance (#1818, #2032, #2073).
  • Track from where modules and subworkflows are installed (#1999).
  • Substitute ModulesCommand and SubworkflowsCommand by ComponentsCommand (#2000).
  • Prevent installation with unsupported Python versions (#2075).
  • Allow other remote URLs not starting with http (#2061)

Modules

  • Update patch file paths if the modules directory has the old structure (#1878).
  • Don't write to modules.json file when applying a patch file during nf-core modules update (#2017).

Subworkflows

  • Add subworkflow commands create-test-yml, create and install (#1897).
  • Update subworkflows install so it installs also imported modules and subworkflows (#1904).
  • check_up_to_date() function from modules_json.py also checks for subworkflows (#1934).
  • Add tests for nf-core subworkflows install command (#1996).
  • Function create() from modules_json.py adds also subworkflows to modules.json file (#2005).
  • Add nf-core subworkflows update command (#2019).

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

Template

  • Add template for subworkflows
  • 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)
  • Improve template customisation documentation (#1821)
  • 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
  • Add nf-core subworkflows create command

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)

Template

  • Update GitHub actions to use nodejs16 (#1944)

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)
  • Make nf-core create fail if Git default branch name is dev or TEMPLATE (#1705)
  • Convert console snippets to bash snippets in the template where applicable (#1729)
  • Add branch field to module entries in modules.json to record what branch a module was installed from (#1728)
  • Add customisation option to remove all GitHub support with nf-core create (#1766)

Linting

  • Check that the .prettierignore file exists and that starts with the same content.
  • Update readme.py nf version badge validation regexp to accept any signs before version number (#1613)
  • Add isort configuration and GitHub workflow (#1538)
  • Use black also to format python files in workflows (#1563)
  • Add check for mimetype in the input parameter. (#1647)
  • Check that the singularity and docker tags are parsable. Add --fail-warned flag to nf-core modules lint (#1654)
  • Handle exception in nf-core modules lint when process name doesn't start with process (#1733)

General

  • Remove support for Python 3.6 (#1680)
  • Add support for Python 3.9 and 3.10 (#1680)
  • Invoking Python with optimizations no longer affects the program control flow (#1685)
  • Update readme to drop --key option from nf-core modules list and add the new pattern syntax
  • Add --fail-warned flag to nf-core lint to make warnings fail (#1593)
  • Add --fail-warned flag to pipeline linting workflow (#1593)
  • Updated the nf-core package requirements (#1620, #1757, #1756)
  • Remove dependency of the mock package and use unittest.mock instead (#1696)
  • Fix and improve broken test for Singularity container download (#1622)
  • Use $XDG_CACHE_HOME or ~/.cache instead of $XDG_CONFIG_HOME or ~/config/ as base directory for API cache
  • Switch CI to use setup-nextflow action to install Nextflow (#1650)
  • Add tests for nf-core modules update and ModulesJson.
  • Add CI for GitLab remote #1646
  • Add CITATION.cff #361
  • Allow customization of the nf-core pipeline template when using nf-core create (#1548)
  • Add Refgenie integration: updating of nextflow config files with a refgenie database (#1090)
  • Fix --key option in nf-core lint when supplying a module lint test name (#1681)
  • Add no_git=True when creating a new pipeline and initialising a git repository is not needed in nf-core lint and nf-core bump-version (#1709)
  • Move strip_ansi_code function in lint to utils.py
  • Simplify control flow and don't use equality comparison for None and booleans
  • Replace use of the deprecated distutils Version object with that from packaging (#1735)
  • Add code to cancel CI run if a new run starts (#1760)
  • CI for the API docs generation now uses the ubuntu-latest base image (#1762)
  • Add option to hide progress bars in nf-core lint and nf-core modules lint with --hide-progress.

Modules

  • Add --fix-version flag to nf-core modules lint command to update modules to the latest version (#1588)
  • Fix a bug in the regex extracting the version from biocontainers URLs (#1598)
  • Update how we interface with git remotes. (#1626)
  • Add prompt for module name to nf-core modules info (#1644)
  • Update docs with example of custom git remote (#1645)
  • Command nf-core modules test obtains module name suggestions from installed modules (#1624)
  • Add --base-path flag to nf-core modules to specify the base path for the modules in a remote. Also refactored modules.json code. (#1643) Removed after (#1754)
  • Rename methods in ModulesJson to remove explicit reference to modules.json
  • Fix inconsistencies in the --save-diff flag nf-core modules update. Refactor nf-core modules update (#1536)
  • Fix bug in ModulesJson.check_up_to_date causing it to ask for the remote of local modules
  • Handle errors when updating module version with nf-core modules update --fix-version (#1671)
  • Make nf-core modules update --save-diff work when files were created or removed (#1694)
  • Get the latest common build for Docker and Singularity containers of a module (#1702)
  • Add short option for --no-pull option in nf-core modules
  • Add nf-core modules patch command (#1312)
  • Add support for patch in nf-core modules update command (#1312)
  • Add support for patch in nf-core modules lint command (#1312)
  • Add support for custom remotes in nf-core modules lint (#1715)
  • Make nf-core modules commands work with arbitrary git remotes (#1721)
  • Add links in README.md for info and patch commands (#1722])
  • Fix misc. issues with --branch and --base-path (#1726)
  • Add branch field to module entries in modules.json to record what branch a module was installed from (#1728)
  • Fix broken link in nf-core modules info(#1745)
  • Fix unbound variable issues and minor refactoring #1742
  • Recreate modules.json file instead of complaining about incorrectly formatted file. (#1741
  • Add support for patch when creating modules.json file (#1752)

v2.4.1 - Cobolt Koala Patch - [2022-05-16]

  • Patch release to try to fix the template sync (#1585)
  • Avoid persistent temp files from pytests (#1566)
  • Add option to trigger sync manually on just nf-core/testpipeline

v2.4 - Cobolt Koala - [2022-05-16]

Template

  • Read entire lines when sniffing the samplesheet format (fix #1561)
  • Add actions workflow to respond to @nf-core-bot fix linting comments on pipeline PRs
  • Fix Prettier formatting bug in completion email HTML template (#1509)
  • Fix bug in pipeline readme logo URL
  • Set the default DAG graphic output to HTML to have a default that does not depend on Graphviz being installed on the host system (#1512).
  • Removed retry strategy for AWS tests CI, as Nextflow now handles spot instance retries itself
  • Add .prettierignore file to stop Prettier linting tests from running over test files
  • Made module template test command match the default used in nf-core modules create-test-yml (#1562)
  • Removed black background from Readme badges now that GitHub has a dark mode, added Tower launch badge.
  • Don't save md5sum for versions.yml when running nf-core modules create-test-yml (#1511)

General

  • Add actions workflow to respond to @nf-core-bot fix linting comments on nf-core/tools PRs
  • Use $XDG_CONFIG_HOME or ~/.config/nf-core instead of ~/.nfcore for API cache (the latter can be safely deleted)
  • Consolidate GitHub API calls into a shared function that uses authentication from the gh GitHub cli tool or GITHUB_AUTH_TOKEN to avoid rate limiting (#1499)
  • Add an empty line to modules.json, params.json and nextflow-schema.json when dumping them to avoid prettier errors.
  • Remove empty JSON schema definition groups to avoid usage errors (#1419)
  • Bumped the minimum version of rich from v10 to v10.7.0

Modules

  • Add a new command nf-core modules mulled which can generate the name for a multi-tool container image.
  • Add a new command nf-core modules test which runs pytests locally.
  • Print include statement to terminal when modules install (#1520)
  • Allow follow links when generating test.yml file with nf-core modules create-test-yml (1570)
  • Escaped test run output before logging it, to avoid a rich MarkupError

Linting

  • Don't allow a .nf-core.yaml file, should be .yml (#1515).
  • shell blocks now recognised to avoid error when: condition has too many lines (#1557)
  • Fixed error when using comments after input tuple lines (#1542)
  • Don't lint the shell block when script is used (1558)
  • Check that template is used in script blocks
  • Tweaks to CLI output display of lint results

v2.3.2 - Mercury Vulture Fixed Formatting - [2022-03-24]

Very minor patch release to fix the full size AWS tests and re-run the template sync, which partially failed due to GitHub pull-requests being down at the time of release.

Template

  • Updated the AWS GitHub actions to let nf-core/tower-action use it's defaults for pipeline and git sha (#1488)
  • Add prettier editor extension to gitpod.yml in template (#1485)
  • Remove traces of markdownlint in the template (#1486
  • Remove accidentally added line in CHANGELOG.md in the template (#1487)
  • Update linting to check that .editorconfig is there and .yamllint.yml isn't.

v2.3.1 - Mercury Vulture Formatting - [2022-03-23]

This patch release is primarily to address problems that we had in the v2.3 release with code linting. Instead of resolving those specific issues, we chose to replace the linting tools (markdownlint, yamllint) with a new tool: Prettier

This is a fairly major change and affects a lot of files. However, it will hopefully simplify future usage. Prettier can auto-format many different file formats (for pipelines the most relevant are markdown and YAML) and is extensible with plugins (Nextflow, anyone?). It tends to be a bit less strict than markdownlint and yamllint and importantly can fix files for you rather than just complaining.

The sync PR may be a little big because of many major changes (whitespace, quotation mark styles etc). To help with the merge, we highly recommend running Prettier on your pipeline's codebase before attempting the template merge. If you take this approach, please copy .editorconfig and .prettierrc.yml from the template to your pipeline root first, as they configure the behaviour of Prettier.

To run Prettier, go to the base of the repository where .editorconfig and .prettierrc.yml are located. Make sure your git status is clean so that the changes don't affect anything you're working on and run:

prettier --write .

This runs Prettier and tells it to fix any issues it finds in place.

Please note that there are many excellent integrations for Prettier available, for example VSCode can be set up to automatically format files on save.

Template

  • Replace markdownlint and yamllint with Prettier for linting formatting / whitespace (#1470)
  • Add CI test using editorconfig-checker for other file types to look for standardised indentation and formatting (#1476)
  • Add md5sum check of versions.yml to test.yml on the modules template.
  • Update bundled module wrappers to latest versions (#1462)
  • Renamed assets/multiqc_config.yaml to assets/multiqc_config.yml (yml not yaml) (#1471)

General

  • Convert nf-core/tools API / lint test documentation to MyST (#1245)
  • Build documentation for the nf-core modules lint tests (#1250)
  • Fix some colours in the nf-core/tools API docs (#1467)
  • Install tools inside GitPod Docker using the repo itself and not from Conda.
  • Rewrite GitHub Actions workflow for publishing the GitPod Docker image.
  • Improve config for PyTest so that you can run pytest instead of pytest tests/ (#1461)
  • New pipeline lint test multiqc_config that checks YAML structure instead of basic file contents (#1461)
  • Updates to the GitPod docker image to install the latest version of nf-core/tools

v2.3 - Mercury Vulture - [2022-03-15]

Template

  • 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)
  • Add pipeline description and authors between triple quotes to avoid errors with apostrophes (#2066, #2104)

General

  • 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)
  • Modified the CSS overriding sphinx_rtd_theme default colors to fix some glitches in the API documentation (#1294)

Modules

  • New command nf-core modules info that prints nice documentation about a module to the terminal ✨ (#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)

v2.2 - Lead Liger - [2021-12-14]

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 modules_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)
  • 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)

v2.1 - Zinc Zebra - [2021-07-27]

Template

  • Correct regex pattern for file names in nextflow_schema.json
  • Remove . from nf-core/tools command examples
  • Update Nextflow installation link in pipeline template (#1201)
  • Command hostname is not portable [#1212]
  • Changed how singularity and docker links are written in template to avoid duplicate links

General

  • Changed names of some flags with -r as short options to make the flags more consistent between commands.

Modules

  • Added consistency checks between installed modules and modules.json (#1199)
  • Added support excluding or specifying version of modules in .nf-core.yml when updating with nf-core modules install --all (#1204)
  • Created nf-core modules update and removed updating options from nf-core modules install
  • Added missing function call to nf-core lint (#1198)
  • Fix nf-core lint not filtering modules test when run with --key (#1203)
  • Fixed nf-core modules install not working when installing from branch with -b (#1218)
  • Added prompt to choose between updating all modules or named module in nf-core modules update
  • Check if modules is installed before trying to update in nf-core modules update
  • Verify that a commit SHA provided with --sha exists for install/update commands
  • Add new-line to main.nf after bump-versions command to make ECLint happy

v2.0.1 - Palladium Platypus Junior - [2021-07-13]

Template

  • Critical tweak to add --dir declaration to nf-core lint GitHub Actions linting.yml workflow

General

  • Add --dir declaration to nf-core sync GitHub Actions sync.yml workflow

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)

v1.14 - Brass Chicken 🐔 - [2021-05-11]

Template

  • Add the implicit workflow declaration to main.nf DSL2 template [#1056]
  • 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

v1.13.3 - Copper Crocodile Resurrection 🐊 - [2021-03-24]

  • Running tests twice with nf-core modules create-test-yml to catch unreproducible md5 sums [#890]
  • 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
  • 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

v1.13.2 - Copper Crocodile CPR 🐊 🤕 - [2021-03-23]

  • Make module template pass the EC linter [#953]
  • 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]

v1.13.1 - Copper Crocodile Patch 🐊 🏴‍☠️ - [2021-03-19]

  • 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

v1.13 - Copper Crocodile - [2021-03-18]

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]

v1.12.1 - Silver Dolphin - [2020-12-03]

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]

v1.12 - Mercury Weasel - [2020-11-19]

Tools helper code

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.

v1.11 - Iron Tiger - [2020-10-27]

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

v1.10.2 - Copper Camel (brought back from the dead) - [2020-07-31]

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]

v1.10.1 - Copper Camel (patch) - [2020-07-30]

Patch release to fix the automatic template synchronisation, which failed in the v1.10 release.

  • Improved logging: nf-core --log-file log.txt now saves a verbose log to disk.
  • nf-core/tools GitHub Actions pipeline sync now uploads verbose log as an artifact.
  • Sync - fixed several minor bugs, made logging less verbose.
  • Python Rich library updated to >=4.2.1
  • Hopefully fix git config for pipeline sync so that commit comes from @nf-core-bot
  • Fix sync auto-PR text indentation so that it doesn't all show as code
  • Added explicit flag --show-passed for nf-core lint instead of taking logging verbosity

v1.10 - Copper Camel - [2020-07-30]

Pipeline schema

This release of nf-core/tools introduces a major change / new feature: pipeline schema. These are JSON Schema files that describe all of the parameters for a given pipeline with their ID, a description, a longer help text, an optional default value, a variable type (eg. string or boolean) and more.

The files will be used in a number of places:

  • Automatic validation of supplied parameters when running pipelines
    • Pipeline execution can be immediately stopped if a required param is missing, or does not conform to the patterns / allowed values in the schema.
  • Generation of pipeline command-line help
    • Running nextflow run <pipeline> --help will use the schema to generate a help text automatically
  • Building online documentation on the nf-core website
  • Integration with 3rd party graphical user interfaces

To support these new schema files, nf-core/tools now comes with a new set of commands: nf-core schema.

  • Pipeline schema can be generated or updated using nf-core schema build - this takes the parameters from the pipeline config file and prompts the developer for any mismatch between schema and pipeline.
    • Once a skeleton Schema file has been built, the command makes use of a new nf-core website tool to provide a user friendly graphical interface for developers to add content to their schema: https://nf-co.re/pipeline_schema_builder
  • Pipelines will be automatically tested for valid schema that describe all pipeline parameters using the nf-core schema lint command (also included as part of the main nf-core lint command).
  • Users can validate their set of pipeline inputs using the nf-core schema validate command.

In addition to the new schema commands, the nf-core launch command has been completely rewritten from scratch to make use of the new pipeline schema. This command can use either an interactive command-line prompt or a rich web interface to help users set parameters for a pipeline run.

The parameter descriptions and help text are fully used and embedded into the launch interfaces to make this process as user-friendly as possible. We hope that it's particularly well suited to those new to nf-core.

Whilst we appreciate that this new feature will add a little work for pipeline developers, we're excited at the possibilities that it brings. If you have any feedback or suggestions, please let us know either here on GitHub or on the nf-core #json-schema Slack channel.

Python code formatting

We have adopted the use of the Black Python code formatter. This ensures a harmonised code formatting style throughout the package, from all contributors. If you are editing any Python code in nf-core/tools you must now pass the files through Black when making a pull-request. See .github/CONTRIBUTING.md for details.

Template

  • Add --publish_dir_mode parameter #585
  • Isolate R library paths to those in container #541
  • Added new style of pipeline parameters JSON schema to pipeline template
  • Add ability to attach MultiQC reports to completion emails when using mail
  • Update output.md and add in 'Pipeline information' section describing standard NF and pipeline reporting.
  • Build Docker image using GitHub Actions, then push to Docker Hub (instead of building on Docker Hub)
  • Add Slack channel badge in pipeline README
  • Allow multiple container tags in ci.yml if performing multiple tests in parallel
  • Add AWS CI tests and full tests GitHub Actions workflows
  • Update AWS CI tests and full tests secrets names
  • Added macs_gsize for danRer10, based on this post
  • Add information about config files used for workflow execution (workflow.configFiles) to summary
  • Fix markdown_to_html.py to work with Python 2 and 3.
  • Change params.reads -> params.input
  • Adding TODOs and MultiQC process in DSL2 template
  • Change params.readPaths -> params.input_paths
  • Added a .github/.dockstore.yml config file for automatic workflow registration with dockstore.org

Linting

  • Refactored PR branch tests to be a little clearer.
  • Linting error docs explain how to add an additional branch protecton rule to the branch.yml GitHub Actions workflow.
  • Adapted linting docs to the new PR branch tests.
  • Failure for missing the readme bioconda badge is now a warn, in case this badge is not relevant
  • Added test for template {{ cookiecutter.var }} placeholders
  • Fix failure when providing version along with build id for Conda packages
  • New --json and --markdown options to print lint results to JSON / markdown files
  • Linting code now automatically posts warning / failing results to GitHub PRs as a comment if it can
  • Added AWS GitHub Actions workflows linting
  • Fail if params.input isn't defined.
  • Beautiful new progress bar to look at whilst linting is running and awesome new formatted output on the command line 😍
  • Tests looking for TODO strings should now ignore editor backup files. #477

nf-core/tools Continuous Integration

  • Added CI test to check for PRs against master in tools repo
  • CI PR branch tests fixed & now automatically add a comment on the PR if failing, explaining what is wrong
  • Move some of the issue and PR templates into HTML <!-- comments --> so that they don't show in issues / PRs

Other

  • Describe alternative installation method via conda with conda env create
  • nf-core/tools version number now printed underneath header artwork
  • Bumped Conda version shipped with nfcore/base to 4.8.2
  • Added log message when creating new pipelines that people should talk to the community about their plans
  • Fixed 'on completion' emails sent using the mail command not containing body text.
  • Improved command-line help text for nf-core/tools
  • nf-core list now hides archived pipelines unless --show_archived flag is set
  • Command line tools now checks if there is a new version of nf-core/tools available
    • Disable this by setting the environment variable NFCORE_NO_VERSION_CHECK, eg. export NFCORE_NO_VERSION_CHECK=1
  • Better command-line output formatting of nearly all nf-core commands using rich

v1.9 - Platinum Pigeon - [2020-02-20]

Continuous integration

  • Travis CI tests are now deprecated in favor of GitHub Actions within the pipeline template.
    • nf-core bump-version support has been removed for .travis.yml
    • nf-core lint now fails if a .travis.yml file is found
  • Ported nf-core/tools Travis CI automation to GitHub Actions.
  • Fixed the build for the nf-core/tools API documentation on the website

Template

  • Rewrote the documentation markdown > HTML conversion in Python instead of R
  • Fixed rendering of images in output documentation #391
  • Removed the requirement for R in the conda environment
  • Make params.multiqc_config give an additional MultiQC config file instead of replacing the one that ships with the pipeline
  • Ignore only tests/ and testing/ directories in .gitignore to avoid ignoring test.config configuration file
  • Rephrase docs to promote usage of containers over Conda to ensure reproducibility
  • Stage the workflow summary YAML file within MultiQC work directory

Linting

  • Removed linting for CircleCI
  • Allow any one of params.reads or params.input or params.design before warning
  • Added whitespace padding to lint error URLs
  • Improved documentation for lint errors
  • Allow either >= or !>= in nextflow version checks (the latter exits with an error instead of just warning) #506
  • Check that manifest.version ends in dev and throw a warning if not
    • If running with --release check the opposite and fail if not
  • Tidied up error messages and syntax for linting GitHub actions branch tests
  • Add YAML validator
  • Don't print test results if we have a critical error

Other

  • Fix automatic synchronisation of the template after releases of nf-core/tools
  • Improve documentation for installing nf-core/tools
  • Replace preprint by the new nf-core publication in Nature Biotechnology 🍾
  • Use stderr instead of stdout for header artwork
  • Tolerate unexpected output from nextflow config command
  • Add social preview image
  • Added a release checklist for the tools repo

v1.8 - Black Sheep - [2020-01-27]

Continuous integration

  • GitHub Actions CI workflows are now included in the template pipeline
    • Please update these files to match the existing tests that you have in .travis.yml
  • Travis CI tests will be deprecated from the next tools release
  • Linting will generate a warning if GitHub Actions workflows do not exist and if applicable to remove Travis CI workflow file i.e. .travis.yml.

Tools helper code

  • Refactored the template synchronisation code to be part of the main nf-core tool
  • nf-core bump-version now also bumps the version string of the exported conda environment in the Dockerfile
  • Updated Blacklist of synced pipelines
  • Ignore pre-releases in nf-core list
  • Updated documentation for nf-core download
  • Fixed typo in nf-core launch final command
  • Handle missing pipeline descriptions in nf-core list
  • Migrate tools package CI to GitHub Actions

Linting

  • Adjusted linting to enable patch branches from being tested
  • Warn if GitHub Actions workflows do not exist, warn if .travis.yml and circleCI are there
  • Lint for Singularity file and raise error if found #458
  • Added linting of GitHub Actions workflows linting.yml, ci.yml and branch.yml
  • Warn if pipeline name contains upper case letters or non alphabetical characters #85
  • Make CI tests of lint code pass for releases

Template pipeline

  • Fixed incorrect paths in iGenomes config as described in issue #418
  • Fixed incorrect usage of non-existent parameter in the template #446
  • Add UCSC genomes to igenomes.config and add paths to all genome indices
  • Change maxMultiqcEmailFileSize parameter to max_multiqc_email_size
  • Export conda environment in Docker file #349
  • Change remaining parameters from camelCase to snake_case #39
    • --singleEnd to --single_end
    • --igenomesIgnore to --igenomes_ignore
    • Having the old camelCase versions of these will now throw an error
  • Add autoMounts=true to default singularity profile
  • Add in markdownlint checks that were being ignored by default
  • Disable ansi logging in the travis CI tests
  • Move paramssection from base.config to nextflow.config
  • Use env scope to export PYTHONNOUSERSITE in nextflow.config to prevent conflicts with host Python environment
  • Bump minimum Nextflow version to 19.10.0 - required to properly use env scope in nextflow.config
  • Added support for nf-tower in the travis tests, using public mailbox nf-core@mailinator.com
  • Add link to Keep a Changelog and Semantic Versioning to CHANGELOG
  • Adjusted .travis.yml checks to allow for patch branches to be tested
  • Add Python 3.7 dependency to the environment.yml file
  • Remove awsbatch profile cf nf-core/configs#71
  • Make scrape_software_versions.py compatible with Python3 to enable miniconda3 in base image PR
  • Add GitHub Actions workflows and respective linting
  • Add NXF_ANSI_LOG as global environment variable to template GitHub Actions CI workflow
  • Fixed global environment variable in GitHub Actions CI workflow
  • Add --awscli parameter
  • Add README.txt path for genomes in igenomes.config nf-core/atacseq#75
  • Fix buggy ANSI codes in pipeline summary log messages
  • Add a TODO line in the new GitHub Actions CI test files

Base Docker image

  • Use miniconda3 instead of miniconda for a Python 3k base environment
    • If you still need Python 2 for your pipeline, add conda-forge::python=2.7.4 to the dependencies in your environment.yml
  • Update conda version to 4.7.12

Other

  • Updated Base Dockerfile to Conda 4.7.10
  • Entirely switched from Travis-Ci.org to Travis-Ci.com for template and tools
  • Improved core documentation (-profile)

v1.7 - Titanium Kangaroo - [2019-10-07]

Tools helper code

  • The tools create command now sets up a TEMPLATE and a dev branch for syncing
  • Fixed issue 379
  • nf-core launch now uses stable parameter schema version 0.1.0
  • Check that PR from patch or dev branch is acceptable by linting
  • Made code compatible with Python 3.7
  • The download command now also fetches institutional configs from nf-core/configs
  • When listing pipelines, a nicer message is given for the rare case of a detached HEAD ref in a locally pulled pipeline. #297
  • The download command can now compress files into a single archive.
  • nf-core create now fetches a logo for the pipeline from the nf-core website
  • The readme should now be rendered properly on PyPI.

Syncing

  • Can now sync a targeted pipeline via command-line
  • Updated Blacklist of synced pipelines
  • Removed chipseq from Blacklist of synced pipelines
  • Fixed issue #314

Linting

  • If the container slug does not contain the nf-core organisation (for example during development on a fork), linting will raise a warning, and an error with release mode on

Template pipeline

  • Add new code for Travis CI to allow PRs from patch branches too
  • Fix small typo in central readme of tools for future releases
  • Small code polishing + typo fix in the template main.nf file
  • Header ANSI codes no longer print [2m to console when using -with-ansi
  • Switched to yaml.safe_load() to fix PyYAML warning that was thrown because of a possible exploit
  • Add nf-core citation
  • Add proper nf-core logo for tools
  • Add Quick Start section to main README of template
  • Fix Docker RunOptions to get UID and GID set in the template
  • Dockerfile now specifically uses the proper release tag of the nfcore/base image
  • Use file instead of new File to avoid weird behavior such as making an s3:/ directory locally when using an AWS S3 bucket as the --outdir.
  • Fix workflow.onComplete() message when finishing pipeline
  • Update URL for joining the nf-core slack to https://nf-co.re/join/slack
  • Add GitHub Action for CI and Linting
  • Increased default time limit to 4h
  • Add direct link to the pipeline slack channel in the contribution guidelines
  • Add contributions and support heading with links to contribution guidelines and link to the pipeline slack channel in the main README
  • Fix Parameters JSON due to new versionized structure
  • Added conda-forge::r-markdown=1.1 and conda-forge::r-base=3.6.1 to environment
  • Plain-text email template now has nf-core ASCII artwork
  • Template configured to use logo fetched from website
  • New option --email_on_fail which only sends emails if the workflow is not successful
  • Add file existence check when checking software versions
  • Fixed issue #165 - Use checkIfExists
  • Consistent spacing for if statements
  • Add sensible resource labels to base.config

Other

  • Bump conda to 4.6.14 in base nf-core Dockerfile
  • Added a Code of Conduct to nf-core/tools, as only the template had this before
  • TravisCI tests will now also start for PRs from patch branches, to allow fixing critical issues without making a new major release

v1.6 - Brass Walrus - [2020-04-09]

Syncing

  • Code refactoring to make the script more readable
  • No travis build failure anymore on sync errors
  • More verbose logging

Template pipeline

  • awsbatch work-dir checking moved to nextflow itself. Removed unsatisfiable check in main.nf template.
  • Fixed markdown linting
  • Tools CI testing now runs markdown lint on compiled template pipeline
  • Migrated large portions of documentation to the nf-core website
  • Removed Gitter references in .github/ directories for tools/ and pipeline template.
  • Changed scrape_software_versions.py to output .csv file
  • Added export_plots parameter to multiqc config
  • Corrected some typos as listed here to Guidelines

Tools helper code

  • Drop nf-core/rnaseq from blacklist.json to make template sync available
  • Updated main help command to sort the subcommands in a more logical order
  • Updated readme to describe the new nf-core launch command
  • Fix bugs in nf-core download
    • The latest release is now fetched by default if not specified
    • Downloaded pipeline files are now properly executable.
  • Fixed bugs in nf-core list
    • Sorting now works again
    • Output is partially coloured (better highlighting out of date pipelines)
    • Improved documentation
  • Fixed bugs in nf-core lint
    • The order of conda channels is now correct, avoiding occasional erroneous errors that packages weren't found (#207)
    • Allow edge versions in nf-core pipelines
  • Add reporting of ignored errored process
    • As a solution for #103)
  • Add Bowtie2 and BWA in iGenome config file template

v1.5 - Iron Shark - [2019-03-13]

Template pipeline

  • Dropped Singularity file
  • Summary now logs details of the cluster profile used if from nf-core/configs
  • Dockerhub is used in favor of Singularity Hub for pulling when using the Singularity profile
  • Changed default container tag from latest to dev
  • Brought the logo to life
  • Change the default filenames for the pipeline trace files
  • Remote fetch of nf-core/configs profiles fails gracefully if offline
  • Remove params.container and just directly define process.container now
  • Completion email now includes MultiQC report if not too big
  • params.genome is now checked if set, to ensure that it's a valid iGenomes key
  • Together with nf-core/configs, helper function now checks hostname and suggests a valid config profile
  • awsbatch executor requires the tracedir not to be set to an s3 bucket.

Tools helper code

  • New nf-core launch command to interactively launch nf-core pipelines from command-line

    • Works with a parameters.settings.json file shipped with each pipeline
    • Discovers additional params from the pipeline dynamically

  • Drop Python 3.4 support

  • nf-core list now only shows a value for "is local latest version" column if there is a local copy.

  • Lint markdown formatting in automated tests

    • Added markdownlint-cli for checking Markdown syntax in pipelines and tools repo

  • Syncing now reads from a blacklist.json in order to exclude pipelines from being synced if necessary.

  • Added nf-core tools API description to assist developers with the classes and functions available.

    • Docs are automatically built by Travis CI and updated on the nf-co.re website.

  • Introduced test for filtering remote workflows by keyword.

  • Build tools python API docs

    • Use Travis job for api doc generation and publish

  • nf-core bump-version now stops before making changes if the linting fails

  • Code test coverage

    • Introduced test for filtering remote workflows by keyword

  • Linting updates

    • Now properly searches for conda packages in default channels
    • Now correctly validates version pinning for packages from PyPI
    • Updates for changes to process.container definition

Other

  • Bump conda to 4.6.7 in base nf-core Dockerfile

v1.4 - Tantalum Butterfly - [2018-12-12]

Template pipeline

  • Institutional custom config profiles moved to github nf-core/configs
    • These will now be maintained centrally as opposed to being shipped with the pipelines in conf/
    • Load base.config by default for all profiles
    • Removed profiles named standard and none
    • Added parameter --igenomesIgnore so igenomes.config is not loaded if parameter clashes are observed
    • Added parameter --custom_config_version for custom config version control. Can use this parameter to provide commit id for reproducibility. Defaults to master
    • Deleted custom configs from template in conf/ directory i.e. uzh.config, binac.config and cfc.config
  • multiqc_config and output_md are now put into channels instead of using the files directly (see issue #222)
  • Added local.md to cookiecutter template in docs/configuration/. This was referenced in README.md but not present.
  • Major overhaul of docs to add/remove parameters, unify linking of files and added description for providing custom configs where necessary
  • Travis: Pull the dev tagged docker image for testing
  • Removed UPPMAX-specific documentation from the template.

Tools helper code

  • Make Travis CI tests fail on pull requests if the CHANGELOG.md file hasn't been updated
  • Minor bugfixing in Python code (eg. removing unused import statements)
  • Made the web requests caching work on multi-user installations
  • Handle exception if nextflow isn't installed
  • Linting: Update for Travis: Pull the dev tagged docker image for testing

v1.3 - Citreous Swordfish - [2018-11-21]

  • nf-core create command line interface updated
    • Interactive prompts for required arguments if not given
    • New flag for workflow author
  • Updated channel order for bioconda/conda-forge channels in environment.yaml
  • Increased code coverage for sub command create and licenses
  • Fixed nasty dependency hell issue between pytest and py package in Python 3.4.x
  • Introduced .coveragerc for pytest-cov configuration, which excludes the pipeline template now from being reported
  • Fix 189: Check for given conda and PyPi package dependencies, if their versions exist
  • Added profiles for cfc,binac, uzh that can be synced across pipelines
    • Ordering alphabetically for profiles now
  • Added pip install --upgrade pip to .travis.yml to update pip in the Travis CI environment

v1.2 - [2018-10-01]

  • Updated the nf-core release command
    • Now called nf-core bump-versions instead
    • New flag --nextflow to change the required nextflow version instead
  • Template updates
    • Simpler installation of the nf-core helper tool, now directly from PyPI
    • Bump minimum nextflow version to 0.32.0 - required for built in manifest.nextflowVersion check and access to workflow.manifest variables from within nextflow scripts
    • New withName syntax for configs
    • Travis tests fail if PRs come against the master branch, slightly refactored
    • Improved GitHub contributing instructions and pull request / issue templates
  • New lint tests
    • .travis.yml test for PRs made against the master branch
    • Automatic --release option not used if the travis repo is nf-core/tools
    • Warnings if depreciated variables params.version and params.nf_required_version are found
  • New nf-core licences subcommand to show licence for each conda package in a workflow
  • nf-core list now has options for sorting pipeline nicely
  • Latest version of conda used in nf-core base docker image
  • Updated PyPI deployment to correctly parse the markdown readme (hopefully!)
  • New GitHub contributing instructions and pull request template

v1.1 - [2018-08-14]

Very large release containing lots of work from the first nf-core hackathon, held in SciLifeLab Stockholm.

  • The Cookiecutter template has been merged into tools
    • The old repo above has been archived
    • New pipelines are now created using the command nf-core create
    • The nf-core template and associated linting are now controlled under the same version system
  • Large number of template updates and associated linting changes
    • New simplified cookiecutter variable usage
    • Refactored documentation - simplified and reduced duplication
    • Better manifest variables instead of params for pipeline name and version
    • New integrated nextflow version checking
    • Updated travis docker pull command to use tagging to allow release tests to pass
    • Reverted Docker and Singularity syntax to use ENV hack again
  • Improved Python readme parsing for PyPI
  • Updated Travis tests to check that the correct dev branch is being targeted
  • New sync tool to automate pipeline updates
    • Once initial merges are complete, a nf-core bot account will create PRs for future template updates

v1.0.1 - [2018-07-18]

The version 1.0 of nf-core tools cannot be installed from PyPi. This patch fixes it, by getting rid of the requirements.txt plus declaring the dependent modules in the setup.py directly.

v1.0 - [2018-06-12]

Initial release of the nf-core helper tools package. Currently includes four subcommands:

  • nf-core list: List nf-core pipelines with local info
  • nf-core download: Download a pipeline and singularity container
  • nf-core lint: Check pipeline against nf-core guidelines
  • nf-core release: Update nf-core pipeline version number