Published March 15, 2022
| Version 2.3
Software
Open
nf-core/tools: v2.3 - Mercury Vulture
Creators
- Phil Ewels1
- Harshil Patel2
- Kevin Menden3
- Sven F.4
- Erik Danielsson
- Alexander Peltzer5
- Gisela Gabernet6
- Maxime U. Garcia7
- Mahesh Binzer-Panchal8
- Jose Espinosa-Carrasco
- James A. Fellows Yates9
- Matthias Hörtenhuber
- Patrick Hüther
- Gregor Sturm10
- Paolo Cozzi
- FriederikeHanssen3
- Martin Proks
- Marc Jones11
- Sateesh Peri12
- Julianus Pfeuffer13
- Lukas Heumos14
- Olga Botvinnik15
- Stephen Kelly
- Moritz E. Beber16
- Raghu Kamat (RK)
- Robert A. Petit III17
- Anders Jemt
- Konrad Rokicki18
- Maxime Borry19
- Abhinav Sharma20
- 1. Science for Life Laboratory
- 2. Seqera Labs
- 3. QBiC
- 4. QBiC @qbicsoftware
- 5. Boehringer Ingelheim
- 6. @qbicsoftware
- 7. @SciLifeLab | Karolinska Institutet
- 8. @NBISweden
- 9. HKI Jena, MPI-EVA Leipzig
- 10. Medical University of Innsbruck
- 11. The Francis Crick Institute
- 12. Leidos
- 13. FU Berlin
- 14. @theislab @schillerlab @scverse
- 15. @czbiohub
- 16. @UnseenBio
- 17. Wyoming Public Health Laboratory
- 18. HHMI (@JaneliaSciComp)
- 19. Max Planck institute for the Science of Human Evolution
- 20. @seqeralabs @biosharp-dotnet
Description
Another big release that's been coming for quite some time (apologies to all who have been running with dev
for weeks / months).
One or two major bugfixes, such as making nf-core download
work again with the latest DSL2 formats. See below for the full list of changes in this release.
Full Changelog: https://github.com/nf-core/tools/compare/2.2...2.3
Template- Removed mention of
--singularity_pull_docker_container
in pipelineREADME.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 withrepository_type: pipeline
for modules commands - Update igenomes path to the
BWAIndex
to fetch the wholeversion0.6.0
folder instead of only thegenome.fa
file - Remove pinned Node version in the GitHub Actions workflows, to fix errors with
markdownlint
- Bumped
nf-core/tower-action
tov3
and removedpipeline
andrevision
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)
- 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-action
to 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)
- New command
nf-core modules info
that prints nice documentation about a module to the terminal :sparkles: (#1427) - Linting a pipeline now fails instead of warning if a local copy of a module does not match the remote (#1313)
- Fixed linting bugs where warning was incorrectly generated for:
Module does not emit software version
Container versions do not match
input:
/output:
not being specified in module- Allow for containers from other biocontainers resource as defined here
- Fixed traceback when using
stageAs
syntax as defined here - Added
nf-core schema docs
command to output pipline parameter documentation in Markdown format for inclusion in GitHub and other documentation systems (#741) - Allow conditional process execution from the configuration file (#1393)
- Add linting for when condition(#1397)
- Added modules ignored table to
nf-core modules bump-versions
. (#1234) - Added
--conda-package-version
flag for specifying version of conda package innf-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 innextflow.config
(#1418)
Files
nf-core/tools-2.3.zip
Files
(2.7 MB)
Name | Size | Download all |
---|---|---|
md5:08b71895bb345526b5fb2afa43f8797d
|
2.7 MB | Preview Download |
Additional details
Related works
- Is supplement to
- https://github.com/nf-core/tools/tree/2.3 (URL)