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.

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

Feature/nextflow upgrade 23 10 0 #77

Merged
merged 25 commits into from
Mar 27, 2024
Merged

Conversation

BasMonkey
Copy link
Contributor

Refactor of the in- and output variables so that the workflows can be run with Nextflow 23.10.0

Copy link
Contributor

@ellendejong ellendejong left a comment

Choose a reason for hiding this comment

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

Wow, amazing effort to add the val() qualifier everywhere, I approve these changes.

Some changed I would like to see:

  • Long input or output tuples/lines (aka >127 characters)
  • Inconsistency in whitespaces

I do see some inconsistencies in use of whitespaces. Sometimes a whitespace is added:
tuple (.....) vs tuple(...)

And there are some whitespaces before the closing brackets:
tuple(emit: fake) vs tuple ( emit: fake )

and whitespaces after a comma:
val(a),val(b), val(c) vs val(a), val(b), val(c) vs val(a),val(b),val(c)

Could you fix these inconsistencies as well to tuple(val(a), val(b), emit: fake)?

Did you check whether deprecated functions/operators are used anywhere?
https://www.nextflow.io/docs/latest/dsl1.html#channels
https://www.nextflow.io/docs/latest/dsl1.html#operators

GATK/4.1.3.0/VariantFiltration.nf Outdated Show resolved Hide resolved
@BasMonkey BasMonkey requested a review from ellendejong February 9, 2024 09:59
ellendejong
ellendejong previously approved these changes Feb 12, 2024
@melferink melferink requested a review from ellendejong March 11, 2024 11:56
@BasMonkey BasMonkey removed the request for review from ellendejong March 11, 2024 11:57
Copy link
Member

@melferink melferink left a comment

Choose a reason for hiding this comment

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

Ok!

@melferink melferink merged commit ce3291c into develop Mar 27, 2024
@melferink melferink deleted the feature/nextflow_upgrade_23_10_0 branch March 27, 2024 09:02
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
None yet
Projects
None yet
Development

Successfully merging this pull request may close these issues.

4 participants