Bump nf-core from 2.1 to 2.9

[dependabot]

Bumps nf-core from 2.1 to 2.9.

Release notes

Sourced from nf-core's releases.

v2.9 - Chromium Falcon

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)(nf-core/tools#2277) [Contributed by @​nvnieuwk]
• Move registry definitions out of profile scope (#2286)(nf-core/tools#2286)
• Remove aws_tower profile (#2287)(nf-core/tools#2287)
• Fixed the Slack report to include the pipeline name (#2291)
• Fix link in the MultiQC report to point to exact version of output docs (#2298)
• Updates seqeralabs/action-tower-launch to v2.0.0 (#2301)
• Remove schema validation from lib folder and use Nextflow nf-validation plugin instead (#1771)
• Fix parsing of container directive when it is not typical nf-core format (#2306)
• Add ability to specify custom registry for linting modules, defaults to quay.io (#2313)
• Add singularity.registry = 'quay.io' in pipeline template (#2305)
• Add apptainer.registry = 'quay.io' in pipeline template (#2352)
• Bump minimum required NF version in pipeline template from 22.10.1 -> 23.04.0 (#2305)
• Add ability to interpret docker.registry from nextflow.config file. If not found defaults to quay.io. (#2318)
• Add functions to dynamically include pipeline tool citations in MultiQC methods description section for better reporting. (#2326)
• Remove --tracedir parameter (#2290)
• Incorrect config parameter warnings when customising pipeline template (#2333)
• Use markdown syntax in the description for the meta map channels (#2358)

Download

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

Updated CLI parameters

Old parameter	New parameter
new parameter	-d / --download-configuration
new parameter	-t / --tower
-c/ --container	-s / --container-system <VALUE>

... (truncated)

Changelog

Sourced from nf-core's changelog.

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)(nf-core/tools#2277) [Contributed by @​nvnieuwk]
• Move registry definitions out of profile scope (#2286)(nf-core/tools#2286)
• Remove aws_tower profile (#2287)(nf-core/tools#2287)
• Fixed the Slack report to include the pipeline name (#2291)
• Fix link in the MultiQC report to point to exact version of output docs (#2298)
• Updates seqeralabs/action-tower-launch to v2.0.0 (#2301)
• Remove schema validation from lib folder and use Nextflow nf-validation plugin instead (#1771)
• Fix parsing of container directive when it is not typical nf-core format (#2306)
• Add ability to specify custom registry for linting modules, defaults to quay.io (#2313)
• Add singularity.registry = 'quay.io' in pipeline template (#2305)
• Add apptainer.registry = 'quay.io' in pipeline template (#2352)
• Bump minimum required NF version in pipeline template from 22.10.1 -> 23.04.0 (#2305)
• Add ability to interpret docker.registry from nextflow.config file. If not found defaults to quay.io. (#2318)
• Add functions to dynamically include pipeline tool citations in MultiQC methods description section for better reporting. (#2326)
• Remove --tracedir parameter (#2290)
• Incorrect config parameter warnings when customising pipeline template (#2333)
• Use markdown syntax in the description for the meta map channels (#2358)

Download

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

Updated CLI parameters

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

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

Linting

• Warn if container access is denied (#2270)

... (truncated)

Commits

• e5ce6ce Merge pull request #2349 from nf-core/dev
• d74b909 Merge #2353: Download: Add apptainer to the list of false positve container...
• ffd8f64 Merge pull request #2358 from mashehu/add-markdown-to-modules-template
• 464f2fb update changelog
• 7c62700 Update CHANGELOG.md
• b70a034 update changelog
• efbe400 add hint to use markdown in component channel description
• 602e858 Generate new screengrabs with rich-codex
• 12b758c Merge pull request #2356 from mirpedrol/rich-codex
• 6b06ccc remove cd modules
• Additional commits viewable in compare view

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[dependabot]

Superseded by #89.