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

selectROI.py removed as samtools now can do it better and in parallel #243

Merged
merged 3 commits into from
Jul 16, 2020
Merged

selectROI.py removed as samtools now can do it better and in parallel #243

merged 3 commits into from
Jul 16, 2020

Conversation

szilvajuhos
Copy link
Contributor

@szilvajuhos szilvajuhos commented Jul 16, 2020 •
edited
Loading

nf-core/sarek pull request

PR checklist

  • We do not need this obsolete script anymore as samtools can do it better and faster
  • Documentation in docs is updated
  • CHANGELOG.md is updated

@szilvajuhos szilvajuhos requested a review from maxulysse as a code owner July 16, 2020 06:54
@maxulysse
Copy link
Member

Do we have a samtools process to do that?

@szilvajuhos szilvajuhos mentioned this pull request Jul 16, 2020
Closed
@szilvajuhos
Copy link
Contributor Author

samtools view -@48 -L target.bed -o targeted.bam input.bam can do that

@maxulysse
Copy link
Member

ok, we'll think of a process to do that in DSL2 then

maxulysse
maxulysse reviewed Jul 16, 2020
View reviewed changes
CHANGELOG.md Outdated Show resolved Hide resolved
szilvajuhos
szilvajuhos commented Jul 16, 2020
View reviewed changes
Copy link
Contributor Author

@szilvajuhos szilvajuhos left a comment

Choose a reason for hiding this comment

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

sure, sorry for the expandtab

@maxulysse
Copy link
Member

sure, sorry for the expandtab

no worry, there was just a markdown linting error

@maxulysse maxulysse merged commit 1c9454c into nf-core:dev Jul 16, 2020
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@maxulysse maxulysse maxulysse approved these changes

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

Successfully merging this pull request may close these issues.
2 participants
@szilvajuhos @maxulysse