Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Important! Template update for nf-core/tools v2.14.0 #89

Closed
wants to merge 1 commit into from
Closed

Important! Template update for nf-core/tools v2.14.0 #89

wants to merge 1 commit into from

Conversation

nf-core-bot
Copy link
Member

Version 2.14.0 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-2.14.0 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v2.14.0 release page.

@asp8200
Copy link
Contributor

asp8200 commented May 8, 2024

@maxulysse : Should we try and get this merged?

asp8200
asp8200 reviewed May 9, 2024
View reviewed changes
nextflow.config
@@ -16,23 +16,25 @@ params {
genome = null
igenomes_base = 's3://ngi-igenomes/igenomes/'
igenomes_ignore = false
fasta = null// MultiQC options
Copy link
Contributor

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

@maxulysse @mirpedrol : It seems that the PR is running the initialisation of that fasta param to null - why is that?

@mirpedrol
Copy link
Member

It seems that the PR is running the initialisation of that fasta param to null - why is that?

Some versions ago when we introduced the nf-validation plugin we change the order in which we retrieve genomes.
Due to this change, having fasta = null prevents the function to retrieve a fast file from igenomes when using --genome. The solution is to remove the initialisation of the fasta param from nextflow.config.

Note that you will need to add the parameter to validationSchemaIgnoreParams, to avoid nf-validation warnings.

@asp8200 asp8200 force-pushed the nf-core-template-merge-2.14.0 branch from 55cf37e to 24dd736 Compare May 9, 2024 08:43
@nf-core-bot
Copy link
Member Author

Version 2.14.1 of the nf-core/tools pipeline template has just been released. This pull-request is now outdated and has been closed in favour of #91

Please use #91 to merge in the new changes from the nf-core template as soon as possible.

@nf-core-bot nf-core-bot closed this May 9, 2024
@asp8200 asp8200 reopened this May 10, 2024
@asp8200 asp8200 closed this May 10, 2024
@maxulysse maxulysse mentioned this pull request May 10, 2024
Merged
11 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@asp8200 asp8200 asp8200 left review comments

Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
3 participants
@nf-core-bot @asp8200 @mirpedrol