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

update preseq/lcextrap errorStrategy to ignore #7011

Closed
wants to merge 2 commits into from
Closed

update preseq/lcextrap errorStrategy to ignore #7011

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
559ebfb
update errorStrategy to ignore
sateeshperi Nov 18, 2024
b3ffa1d
Merge branch 'master' into fix/preseq-lcextrap
sateeshperi Nov 19, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 1 addition & 1 deletion modules/nf-core/preseq/lcextrap/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
process PRESEQ_LCEXTRAP {
tag "$meta.id"
label 'process_single'
label 'error_retry'
label 'error_ignore'
Copy link
Contributor

Choose a reason for hiding this comment

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

Can we remove the label and make a custom one?

Retry it once, then if it fails the second time we ignore it?

Copy link
Contributor Author

Choose a reason for hiding this comment

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

label 'error_retry_ignore' ?

Copy link
Contributor

Choose a reason for hiding this comment

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

No just define the error strategy at that point 😂

Copy link
Contributor

Choose a reason for hiding this comment

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

Retrying once and then failing sounds great, from what I recall this fails anytime the sample doesn't have enough depth.


conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
Expand Down
2 changes: 0 additions & 2 deletions modules/nf-core/preseq/lcextrap/tests/tags.yml
View file
Open in desktop

This file was deleted.

Loading