nf-core/tools: Changelog

v3.1.1 - Brass Boxfish Patch - [2024-12-20]

Template

Use outputs instead of the environment to pass around values between steps in the Download Test Action (#3351)
Fix pre commit template (#3358)
Set LICENSE copyright to nf-core community (#3366)
fix including modules.config (#3356)

Linting

Linting of pipeline LICENSE file is a warning to allow for author/maintainer names (#3366)

General

Add missing p (#3357)
Use manifest.contributors names if available, otherwise default to manifest.author (#3362)
Properly parse the names form manifest.contributors (#3364)

v3.1.0 - Brass Boxfish - [2024-12-09]

Highlights

We added the new contributors field to the pipeline template manifest.
The nf-core pipelines download command supports ORAS container URIs.
New command nf-core subworkflows patch.

Template

Keep pipeline name in version.yml file (#3223)
Fix Manifest DOI text (#3224)
Do not assume pipeline name is url (#3225)
fix workflow_dispatch trigger and parse more review comments in awsfulltest (#3235)
Add resource limits to Gitpod profile(#3255)
Fix a typo (#3268)
Remove def from nextflow.config and add trace_report_suffix param (#3296)
Move includeConfig 'conf/modules.config' next to includeConfig 'conf/base.config' to not overwrite tests profiles configurations (#3301)
Use params.monochrome_logs in the template and update nf-core components (#3310)
Fix some typos and improve writing in usage.md and CONTRIBUTING.md (#3302)
Add manifest.contributors to nextflow.config (#3311)
Update template components (#3328)
Template: Remove mention of GRCh37 if igenomes is skipped (#3330)
Be more verbose in approval check action (#3338)

Download

First steps towards fixing #3179: Modify prioritize_direct_download() to retain Seqera Singularity https:// Container URIs and hardcode Seqera Containers into gather_registries() (#3244).
Further steps towards fixing #3179: Enable limited support for oras:// container paths (only absolute URIs, no flexible registries like with Docker) and prevent unnecessary image downloads for Seqera Container modules with reconcile_seqera_container_uris() (#3293).
Update dawidd6/action-download-artifact action to v7 (#3306)

Linting

allow mixed str and dict entries in lint config (#3228)
fix meta_yml linting test failing due to module.process_name always being "" (#3317)
fix module section regex matching wrong things (#3321)

Modules

add a panel around diff previews when updating (#3246)

Subworkflows

Add nf-core subworkflows patch command (#2861)
Improve subworkflow nf-test migration warning (#3298)

General

Include .nf-core.yml in nf-core pipelines bump-version (#3220)
create: add shortcut to toggle all switches (#3226)
Remove unrelated values when saving .nf-core file (#3227)
use correct --profile options for nf-core subworkflows test (#3233)
Update GitHub Actions (#3237)
add --dir/-d option to schema commands (#3247)
fix headers in api docs (#3323)
handle new schema structure in nf-core pipelines create-params-file (#3276)
Update Gitpod image to use Miniforge instead of Miniconda(#3274)
Add hint to solve git errors with a synced repo (#3279)
Run pre-commit when testing linting the template pipeline (#3280)
Make CLI prompt less nf-core specific (#3326)
Update gitpod vscode extensions to use nf-core extension pack (#3327)
Remove toList() channel operation from inside onComplete block (#3304)
build: Setup VS Code tests (#3292)
Don't break gitpod.yml with template string (#3332)
rocrate: remove duplicated entries for name and version (#3333)
rocrate: Update crate with version bump and handle new contributor field (#3334)
set default_branch to master for now (#3335)
Set git defaultBranch to master in sync action (#3337)
Add verbose mode to sync action (#3339)

Version updates

chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.12.0 (#3230)
Update codecov/codecov-action action to v5 (#3283)
Update gitpod/workspace-base Docker digest to 12853f7 (#3309)
Update pre-commit hook astral-sh/ruff-pre-commit to v0.8.2 (#3325)

v3.0.2 - Titanium Tapir Patch - [2024-10-11]

Template

Add null/ to .gitignore (#3191)
Parallelize pipeline GHA tests over docker/conda/singularity (#3214)
Fix template_version_comment.yml github action (#3212)
Fix pre-commit linting on pipeline template (#3218)

Linting

Fix bug when linting schema params and when using defaultIgnoreParams (#3213)

General

Use updated pipeline commands in docstrings (#3215)
Disable automatic sync on release, fix handling empty pipeline input (#3217)

v3.0.1 - Titanium Tapir Patch - [2024-10-09]

Template

Fixed an issue where the linting CI action didn't read the correct file (#3202)
Fixed condition for awsfulltest to run (#3203)
Fix too many empty lines added by jinja (#3204 and #3206)
Fix header blocks in local subworkflow including git merge marker-like strings (#3201)
Update included subworkflows and modules (#3208)

v3.0.0 - Titanium Tapir - [2024-10-08]

Highlights

Pipeline commands are renamed from nf-core <command> to nf-core pipelines <command> to follow the same command structure as modules and subworkflows commands.
More customisation for pipeline templates. The template has been divided into features which can be skipped, e.g. you can create a new pipeline without any traces of FastQC in it.
A new Text User Interface app when running nf-core pipelines create to help us guide you through the process better (no worries, you can still use the cli if you give all values as parameters)
We replaced nf-validation with nf-schema in the pipeline template
CI tests now lint with the nf-core tools version matching the template version of the pipeline, to minimise errors in opened PRs with every new tools release.
nf-core licences command is deprecated.
Changed default branch to main.
The structure of nf-core/tools pytests has been updated.
The structure of the API docs has been updated.

Template

Change paths to test data (#2985)
Run awsfulltest on PRs to master with two PR approvals (#3042)
Remove deprecated syntax (#3046)
Use filename in code block for params.yml (#3055)
Remove release announcement for non nf-core pipelines (#3072)
handle template features with a yaml file (#3108, #3112)
add option to exclude code linters for custom pipeline template (#3084)
add option to exclude citations for custom pipeline template (#3101 and #3169)
add option to exclude gitpod for custom pipeline template (#3100)
add option to exclude codespaces from pipeline template (#3105)
add option to exclude multiqc from pipeline template (#3103)
add option to exclude changelog from custom pipeline template (#3104)
add option to exclude license from pipeline template (#3125)
add option to exclude email from pipeline template (#3126)
add option to exclude nf-schema from the template (#3116)
add option to exclude fastqc from pipeline template (#3129)
add option to exclude documentation from pipeline template (#3130)
add option to exclude test configs from pipeline template (#3133)
add option to exclude tower.yml from pipeline template (#3134)
Use nf-schema instead of nf-validation (#3116)
test pipeline with conda and singularity on PRs to master (#3149)
run nf-core lint --release on PRs to master (#3148)
Add tests to ensure all files are part of a template customisation group and all groups are tested (#3099)
Update the syntax of utils_nfcore_pipeline_pipeline local subworkflow (#3166)
Remove if/else block to include igenomes.config (#3168)
Fixed release announcement hashtags for Mastodon (#3099)
Remove try/catch blocks from nextflow.config (#3167)
Extend download_pipeline.yml to count pre-downloaded container images. (#3182)

Linting

Fix linting fail on nfcore_external_java_deps if nf_schema is used (#2976)
Conda module linting: Include package name in log file (#3014)
Remove defaults from conda environment.yml file. (#3029)
Restructure pipeline tests and move pipeline linting into subfolder (#3070)
Fix module linting warning for process_high_memory (#3086)
Linting will now fail when an unpinned plugin is used (#3116)
Linting will now check if the schema is correct for the used validation plugin ([#3116])(#3116)
Linting will now check the use of the right validation plugin include statements in the workflow scripts ([#3116])(#3116)
Full linting for correct use of nf-schema and nf-validation (#3116)
Handle cases where the directory path contains the name of the component (#3147)
Don't test conda environment.yml name attribute (which should no longer be there) (#3161)

Pipeline create command

Allow more special characters on the pipeline name for non-nf-core pipelines (#3008)
Mock git cretentials to generate stable textual snapshots (#3007)
Display input textbox with equally spaced grid (#3038)
Allow numbers in custom pipeline name (#3094)

Components

The modules_nfcore tag in the main.nf.test file of modules/subworkflows now displays the organization name in custom modules repositories (#3005)
Add --migrate_pytest option to nf-core <modules|subworkflows> test command (#3085)
Allow spaces at the beginning of include statements (#3115)
Add option --fix to update the meta.yml file of subworkflows (#3077)

Download

Fully removed already deprecated -t / --tower flag.
Refactored the CLI for consistency (short flag is usually second word, e.g. also for --container-library etc.):

Old parameter	New parameter
`-d` / `--download-configuration`	`-c` / `--download-configuration`
`-p` / `--parallel-downloads`	`-d` / `--parallel-downloads`
new parameter	`-p` / (`--platform`)

General

Change default branch to main for the nf-core/tools repository
Update output of generation script for API docs to new structure (#2988)
Remove rich-codex.yml action, images are now generated on the website repo (#2989)
Add no clobber and put bash options on their own line (#2991)
move pipeline subcommands for v3.0 (#2983)
return directory if base_dir is the root directory (#3003)
Remove nf-core licences command (#3012)
README - absolute image paths (#3013)
Add warning deprecation message to top-level commands (#3036)
move pipeline commands to functions to avoid duplication (#3039)
update output_dir for api docs to new website structure (#3051)
Add --limit-output argument for modules/subworkflow update (#3047)
update api docs to new structure (#3054)
handle new jsonschema error type (#3061)
Fix number of arguments for pipelines_create within the command_create function (#3074)
Add bot action to update textual snapshots and write bot documentation (#3102)
Update gitpod setup (#3136)
fix syncing a pipeline from current directory (#3143)
Patch gitpod conda setup to not use defaults channel (#3159)

Version updates

Update pre-commit hook astral-sh/ruff-pre-commit to v0.6.0 (#3122)
Update gitpod/workspace-base Docker digest to 92dd1bc (#2982)
Update python:3.12-slim Docker digest to 59c7332 (#3124)
Update pre-commit hook pre-commit/mirrors-mypy to v1.11.1 (#3091)
Update to pytest v8 and move it to dev dependencies (#3058)
Update minimal textual version and snapshots (#2998)

v2.14.1 - Tantalum Toad - Patch - [2024-05-09]

Template

Don't cache pip in linting.yml (#2961)
Lint pipelines with the nf-core template version and post comment if it is outdated (#2978)

General

Fix update github action for components in pipeline template (#2968)
Run sync after release on self hosted runners (#2970)

v2.14.0 - Tantalum Toad - [2024-05-08]

Template

Remove fasta default from nextflow.config (#2828)
Update templates to use nf-core/setup-nextflow v2 (#2818)
Link to troubleshooting docs when pipeline fails (#2845)
Add fallback to download_pipeline.yml in case the pipeline does not support stub runs (#2846)
Set topic variable correctly in the mastodon announcement (#2848)
Add a cleanup action to download_pipeline.yml to fix failures caused by inadequate storage space on the runner (#2849)
Update python to 3.12 (#2805)
Remove pyproject.toml from template root
Shorten lines in pipeline template (#2908)
Add a new hidden --pipelines_testdata_base_path parameter to more easily switch locations of test data in test configs (#2931)[#2931]
Permanently activated pipeline-specific institutional configs support for all pipelines without need for manual intervention (#2936)
Template config: conda.channels, not channels (#2950)
Handles multiple DOIs + doi.org resolver from manifest.doi (#2946)
Update included components (#2949)
Update .editorconfig (#2953)

Linting

Only match assignments of params in main.nf and not references like params.aligner == <something> (#2833)
Include test for presence of versions in snapshot (#2888)
Components: set correct sha before running component lint tests (#2952)
Less strict logo comparison (#2956)
Handle request errors more gracefully for actions validation (#2959)

Download

Replace --tower with --platform. The former will remain for backwards compatibility for now but will be removed in a future release. (#2853)
Better error message when GITHUB_TOKEN exists but is wrong/outdated
New --tag argument to add custom tags during a pipeline download (#2938)

Components

Handle more complete list of possible git URL forms (ssh:// and ftp:// prefixes specifically) (#2945)
Fix path in component update script (#2823)

General

Update CI to use nf-core/setup-nextflow v2 (#2819)
Changelog bot: handle also patch version before dev suffix (#2820)
Add force_pr flag to sync, to force a PR even though there are no changes committed (#2822)
Update prettier to 3.2.5 (#2830)
Update GitHub Actions (#2827), (#2902), (#2927), (#2939)
Switch to setup-nf-test (#2834)
Add tests for assignment and referencing of params in main.nf (#2841)
Optimize layers in dockerfile (#2842)
Update python:3.11-slim Docker digest to a2eb07f (#2847)
Strip out mention of "Nextflow Tower" and replace with "Seqera Platform" wherever possible
Fix issue with config resolution that was causing nested configs to behave unexpectedly (#2862)
Fix schema docs console output truncating (#2880)
Ensure path object converted to string before stripping quotes (#2878)
Fix incorrect assertions for called_with on mocks (#2891)
Make cli-provided module/subworkflow names case insensitive (#2869)
Get immediate parent path name for schema creation (#2886)
Remove old references to CUSTOMDUMPSOFTWAREVERSIONS and add linting checks (#2897)
Update pre-commit hook pre-commit/mirrors-mypy to v1.10.0 (#2933)
Update codecov/codecov-action digest to 5ecb98a (#2948)
Update gitpod/workspace-base Docker digest to 124f2b8 (#2943)
fix(collectfile): sort true for methods_description_mqc.yaml (#2947)
chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.4.3 (#2951)
Restructure CHANGELOG.md (#2954)
fix: ensure path object converted to string before stripping quotes (#2878)
Test data uses paths instead of config map (#2877)

v2.13.1 - Tin Puppy Patch - [2024-02-29]

Template

Remove obsolete editor settings in devcontainer.json and gitpod.yml (#2795)
Add nf-test test instructions to contributing and PR template (#2807)
Fix topic extraction step for hashtags in toots (#2810)
Update modules and subworkflows in the template (#2811)
Unpin setup-nextflow and action-tower-launch (#2806)
Add nf-core-version to .nf-core.yml (#2874)

Download

Improved offline container image resolution by introducing symlinks, fixes issues #2751, #2644 and demultiplex#164: (#2768)

Linting

Components

General

chore(deps): update codecov/codecov-action digest to 0cfda1d (#2794)
chore(deps): update gitpod/workspace-base docker digest to c15ee2f (#2799)

v2.13 - Tin Puppy - [2024-02-20]

Template

Add empty line in README.md to fix badges. (#2729)
Replace automatic branch detection in nf-core download CI test with hardcoded dev and input. (#2727)
Add Github Action to automatically cleanup ubuntu-latest runners to fix runner running out of diskspace errors(#2755)
Fix GitHub Actions CI and Linting badges links (#2757)
Add hashtags to release announcement on mastodon (#2761)
update fastqc and multiqc in template (#2776)
template refactoring: remove the lib directory and use nf-core subworkflows (#2736)
use nf-validation to create an input channel from a sample sheet (#2736)

Linting

Make creat-lint-wf composable (#2733)
Add looser comparison when pipeline logos (#2744)
Handle multiple aliases in module imports correctly during linting (#2762)
Switch to markdown based API and error docs (#2758)

Modules

Handle dirty local module repos by force checkout of commits and branches if needed (#2734)
Patch: handle file not found when it is an added file to a module (#2771)
Handle symlinks when migrating pytest (#2770)
Add --profile parameter to nf-test command (#2767)
Reduce the sha length in the nf-core modules list local and add links to the specific commit (#2870)
Add links the nf-core module page and to open the local file in VSCode for module lint results (#2870)

General

fix ignoring changes in partially templated files (e.g. .gitignore) (#2722)
update ruff to 0.2.0 and add it to pre-commit step (#2725)
Update codecov/codecov-action digest to e0b68c6 (#2728)
Update pre-commit hook astral-sh/ruff-pre-commit to v0.2.1 (#2730)
Update python:3.11-slim Docker digest to 2a746e2 (#2743)
Update actions/setup-python action to v5 (#2739)
Update gitpod/workspace-base Docker digest to 45e7617 (#2747)
chore(deps): pin jlumbroso/free-disk-space action to 54081f1 (#2756)
chore(deps): update actions/github-script action to v7 (#2766)
chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.2.2 (#2769)
Update gitpod/workspace-base Docker digest to 728e1fa (#2780)

v2.12.1 - Aluminium Wolf - Patch - [2024-02-01]

Linting

Handle default values of type number from nextflow schema (#2703)
fix ignoring files_unchanged (#2707)

General

Update pre-commit hook astral-sh/ruff-pre-commit to v0.1.15 (#2705)
use types for default value comparison (#2712)
fix changelog titles (#2708)
Print relative path not absolute path in logo cmd log output (#2709)
Update codecov/codecov-action action to v4 (#2713)
Ignore nf-core-bot in renovate PRs (#2716)

v2.12 - Aluminium Wolf - [2024-01-29]

Template

Add a Github Action Workflow to the pipeline template that tests a successful download with nf-core download (#2618)
Use pre-commit to lint files in GitHub CI (#2635)
Use pdiff also on gitpod for nf-test (#2640)
switch to new image syntax in readme (#2645)
Add conda channel order to nextflow.config (#2094)
Fix tyop in pipeline nextflow.config (#2664)
Remove nfcore_external_java_deps.jar from lib directory in pipeline template (#2675)
Add function to check -profile is well formatted (#2678)
Add new pipeline error message pointing to docs when 'requirement exceeds available memory' error message (#2680)
add 👀👍🏻🎉😕 reactions to fix-linting-bot action (#2692)

Linting

Fix linting of a pipeline with patched custom module (#2669)
linting a pipeline also lints the installed subworkflows (#2677)
environment.yml name must be lowercase (#2676)
allow ignoring specific files when template_strings (#2686)
lint nextflow.config default values match the ones specified in nextflow_schema.json (#2684)

Modules

Fix empty json output for nf-core list local (#2668)

General

Run CI-pytests for nf-core tools on self-hosted runners (#2550)
Add Ruff linter and formatter replacing Black, isort and pyupgrade (#2620)
Set pdiff as nf-test differ in Docker image for Gitpod (#2642)
Fix Renovate Dockerfile updating issues (#2648 and #2651)
Add new subcommand nf-core tui, which launches a TUI (terminal user interface) to intuitively explore the command line flags, built using Trogon (#2655)
Add new subcommand: nf-core logo-create to output an nf-core logo for a pipeline (instead of going through the website) (#2662)
Handle api redirects from the old site (#2672)
Remove redundanct v in pipeline version for emails (#2667)
add function to check -profile is well formatted (#2678)
Update pre-commit hook astral-sh/ruff-pre-commit to v0.1.14 (#2674)
Update pre-commit hook pre-commit/mirrors-mypy to v1.8.0 (#2630)
Update mshick/add-pr-comment action to v2 (#2632)
update python image version in docker file (#2636)
Update actions/cache action to v4 (#2666)
Update peter-evans/create-or-update-comment action to v4 (#2683)
Update peter-evans/create-or-update-comment action to v4 (#2695)

v2.11.1 - Magnesium Dragon Patch - [2023-12-20]

Template

Rename release-announcments.yml to release-announcements.yml (#2610)
Fix nextflow.config docker.runOptions (#2607)

General

Only dump modules.json when it is modified (#2609)

v2.11 - Magnesium Dragon - [2023-12-19]

Template

Fix writing files to a remote outdir in the NfcoreTemplate helper functions (#2465)
Fancier syntax highlighting for example samplesheets in the usage.md template (#2503)
Use closure for multiqc ext.args (#2509)
Fix how the modules template references the conda environment file (#2540)
Unset env variable JAVA_TOOL_OPTIONS in gitpod (#2569)
Pin the version of nf-validation (#2579)
Disable process selector warnings by default (#2161)
Remove docker.userEmulation from nextflow.config in pipeline template (#2580)

Download

Add docker:// prefix for absolute container URIs as well (#2576).
Bugfix for AttributeError: ContainerError object has no attribute absoluteURI (#2543).

Linting

Fix incorrectly failing linting if 'modules' was not found in meta.yml (#2447)
Correctly pass subworkflow linting test if COMPONENT.out.versions is used in the script (#2448)
Add pyupgrade to pre-commit config and dev requirements as mentioned in #2200
Check for spaces in modules container URLs (#2452)
Correctly ignore timeline.enabled, report.enabled, trace.enabled, dag.enabled variables when linting a pipeline. (#2507)
Lint nf-test main.nf.test tags include all used components in chained tests (#2572)
Don't fail linting if md5sum for empty files are found in a stub test (#2571)
Check for existence of test profile (#2478)

Modules

Added stub test creation to create_test_yml (#2476)
Replace ModulePatch by ComponentPatch (#2482)
Fixed nf-core modules lint to work with new module structure for nf-test (#2494)
Add option --migrate-pytest to create a module with nf-test taking into account an existing module (#2549)
When installing modules and subworkflows, automatically create the ./modules directory if it doesn't exist (#2563)
When .nf-core.yml is not found create it in the current directory instead of the root filesystem (#2237)
Modules --migrate-pytest copies template scripts (#2568)

Subworkflows

Added stub test creation to create_test_yml (#2476)
Fixed nf-core subworkflows lint to work with new module structure for nf-test (#2494)
Add option --migrate-pytest to create a subworkflow with nf-test taking into account an existing subworkflow (#2549)

General

Update schema build functionality to automatically update defaults which have changed in the nextflow.config(#2479)
Change testing framework for modules and subworkflows from pytest to nf-test (#2490)
bump_version keeps now the indentation level of the updated version entries (#2514)
Add mypy to pre-commit config for the tools repo (#2545)
Use Path objects for ComponentCreate and update the structure of components templates (#2551).
GitPod base image: swap tool installation back to conda from mamba (#2566).
Sort the installed_by list in modules.json (#2570).
Unset env variable JAVA_TOOL_OPTIONS in gitpod (#2569)

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])(#2286)
Remove aws_tower profile ([#2287])(#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 positive 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 when 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 ([#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 account 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 pipeline 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 minimum 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 minimum Nextflow version to 21.10.3
Changed questionary ask() to unsafe_ask() to not catch KeyboardInterrupts (#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 syntax 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 indefinitely
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 specify 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

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.

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 protection 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 😍
- All made using the excellent rich python library - check it out!
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  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

Files

CHANGELOG.md

Latest commit

History

CHANGELOG.md

File metadata and controls

nf-core/tools: Changelog

v3.1.1 - Brass Boxfish Patch - [2024-12-20]

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Linting

General

v3.1.0 - Brass Boxfish - [2024-12-09]

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Linting

Modules

Subworkflows

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Version updates

v3.0.2 - Titanium Tapir Patch - [2024-10-11]

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v3.0.1 - Titanium Tapir Patch - [2024-10-09]

Template

v3.0.0 - Titanium Tapir - [2024-10-08]

Template

Linting

Pipeline create command

Components

Download

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Version updates

v2.14.1 - Tantalum Toad - Patch - [2024-05-09]

Template

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v2.14.0 - Tantalum Toad - [2024-05-08]

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v2.13.1 - Tin Puppy Patch - [2024-02-29]

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v2.13 - Tin Puppy - [2024-02-20]

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v2.12.1 - Aluminium Wolf - Patch - [2024-02-01]

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v2.12 - Aluminium Wolf - [2024-01-29]

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v2.11.1 - Magnesium Dragon Patch - [2023-12-20]

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v2.11 - Magnesium Dragon - [2023-12-19]

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Subworkflows

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

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Subworkflows

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

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