v2.9 - Chromium Falcon + [2023-06-30]

A new big release with new features, template updates and bug fixes. Thanks to all contributors!

🌟 Highlights

• A new nf-core downloadcommand compatible with Nextflow Tower.
• Implementation of the plugin nf-validation for parameter validation in pipeline templates.
• Nextflow version bump to 23.04.0.

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])(#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 positve container strings (#2353).

Updated CLI parameters

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])(https://github.com/nf-core/tools/pull/2278/files)
• 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