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

No scatteron full size tests to avoid issues with in or output files randomly not staged #782

Merged
merged 3 commits into from
Oct 10, 2022
Merged

No scatteron full size tests to avoid issues with in or output files randomly not staged #782

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
2a93482
reduce scatter gather on full size tests
FriederikeHanssen Oct 10, 2022
7089931
update changelog
FriederikeHanssen Oct 10, 2022
f9c382c
BOTH TESTS NEED THIS
FriederikeHanssen Oct 10, 2022
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
1 change: 1 addition & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#762](https://github.com/nf-core/sarek/pull/762) - Back to dev
- [#762](https://github.com/nf-core/sarek/pull/762) - Update deepvariant module
- [#773](https://github.com/nf-core/sarek/pull/773) - Sync `TEMPLATE` with `tools` `2.6`
- [#782](https://github.com/nf-core/sarek/pull/782) - Reduce scatter/gather for full size tests on AWS

### Fixed

Expand Down
7 changes: 4 additions & 3 deletions conf/test_full.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,8 @@ params {

// Other params
tools = 'strelka,mutect2,freebayes,ascat,manta,cnvkit,tiddit,controlfreec,vep'
split_fastq = 20000000
intervals = 's3://nf-core-awsmegatests/sarek/input/S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed'
wes = true
split_fastq = 20000000
intervals = 's3://nf-core-awsmegatests/sarek/input/S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed'
wes = true
nucleotides_per_second = 100000
}
2 changes: 2 additions & 0 deletions conf/test_full_germline.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -21,4 +21,6 @@ params {
tools = 'strelka,freebayes,haplotypecaller,deepvariant,manta,tiddit,cnvkit,vep'

split_fastq = 50000000
nucleotides_per_second = 100000

}