8000 switch germline and somatic full tests by FriederikeHanssen · Pull Request #731 · nf-core/sarek · GitHub
[go: up one dir, main page]
More Web Proxy on the site http://driver.im/
Skip to content

switch germline and somatic full tests #731

New issue

8000 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
merged 2 commits into from
Sep 6, 2022
Merged

switch germline and somatic full tests #731

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
78f7c88
switch germline and somatic full tests
FriederikeHanssen Sep 6, 2022
b6a867e
update changelog
FriederikeHanssen Sep 6, 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 @@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#720](https://github.com/nf-core/sarek/pull/720) - Sync `TEMPLATE` with `tools` `2.5`
- [#723](https://github.com/nf-core/sarek/pull/723) - Sync `TEMPLATE` with `tools` `2.5.1`
- [#730](https://github.com/nf-core/sarek/pull/730) - Reduce number of tests
- [#731](https://github.com/nf-core/sarek/pull/731) - Run the somatic test as default on `-profile test_full`, the germline can be tested with `-profile test_full_somatic`

### Fixed

Expand Down
9 changes: 5 additions & 4 deletions conf/test_full.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,10 +15,11 @@ params {
config_profile_description = 'Full test dataset to check pipeline function'

// Input data for full size test
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/NA12878_WGS_30x_full_test.csv'
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/HCC1395_WXS_somatic_full_test.csv'

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

split_fastq = 50000000
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
}
24 changes: 24 additions & 0 deletions conf/test_full_germline.config
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,24 @@
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Nextflow config file for running full-size tests
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Defines input files and everything required to run a full size pipeline test.

Use as follows:
nextflow run nf-core/sarek -profile test_full_germline,<docker/singularity> --outdir <OUTDIR>

----------------------------------------------------------------------------------------
*/

params {
config_profile_name = 'Full test profile for germline VC'
config_profile_description = 'Full test dataset to check germline VC pipeline function'

// Input data for full size test
input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/NA12878_WGS_30x_full_test.csv'

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

split_fastq = 50000000
}
25 changes: 0 additions & 25 deletions conf/test_full_somatic.config
View file
Open in desktop

This file was deleted.

6 changes: 3 additions & 3 deletions nextflow.config
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -201,9 +201,9 @@ profiles {
executor.cpus = 16
executor.memory = 60.GB
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
test_full_somatic { includeConfig 'conf/test_full_somatic.config' }
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
test_full_germline { includeConfig 'conf/test_full_germline.config' }
}


Expand Down
0