The nf-core framework for community-curated bioinformatics pipelines.

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])(https://github.com/nf-core/tools/pull/2277) [Contributed by @nvnieuwk] Move registry definitions out of profile scope ([#2286])(https://github.com/nf-core/tools/pull/2286) Remove aws_tower profile ([#2287])(https://github.com/nf-core/tools/pull/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 new parameter -l / --container-library --singularity-cache -u / --container-cache-utilisation new parameter -i / --container-cache-index 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 areasIf you use `nf-core tools` in your work, please cite the `nf-core` publicatio