Skip to content

More sensible default for use_annotation_cache_keys #1196

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

Merged
maxulysse merged 1 commit into from
Aug 30, 2023
Merged

More sensible default for use_annotation_cache_keys #1196

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
1 commit
Select commit
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 CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#1158](https://github.com/nf-core/sarek/pull/1158) - Add preprint
- [#1159](https://github.com/nf-core/sarek/pull/1159) - ISMB Poster
- [#1173](https://github.com/nf-core/sarek/pull/1173) - CI tests for VQSR track with stub runs
- [#1122](https://github.com/nf-core/sarek/pull/1122) - Add `annotation cache` functionality
- [#1122](https://github.com/nf-core/sarek/pull/1122), [#1196](https://github.com/nf-core/sarek/pull/1196) - Add `annotation cache` functionality
- [#1184](https://github.com/nf-core/sarek/pull/1184) - Stub-based CI-test of Sentieon joint-germline variant-calling with VQSR

### Changed
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://ngi-igenomes/test-data/sarek/S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed'
wes = true
split_fastq = 20000000
intervals = 's3://ngi-igenomes/test-data/sarek/S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed'
wes = true
use_annotation_cache_keys = true
}
4 changes: 2 additions & 2 deletions conf/test_full_germline.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,6 @@ params {

// Other params
tools = 'strelka,freebayes,haplotypecaller,deepvariant,manta,tiddit,cnvkit,vep'

split_fastq = 50000000
split_fastq = 50000000
use_annotation_cache_keys = true
}
2 changes: 1 addition & 1 deletion nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -83,7 +83,7 @@ params {
spliceai_indel_tbi = null // No spliceai_indel file index
spliceai_snv = null // No spliceai_snv file
spliceai_snv_tbi = null // No spliceai_snv file index
use_annotation_cache_keys = true
use_annotation_cache_keys = false
vep_cache = 's3://annotation-cache/vep_cache/'
vep_custom_args = "--everything --filter_common --per_gene --total_length --offline --format vcf" // Default arguments for VEP
vep_dbnsfp = null // dbnsfp plugin disabled within VEP
Expand Down