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

Add full size test NA12878 #604

Merged
merged 7 commits into from
Jun 30, 2022
Merged

Add full size test NA12878 #604

Show file tree
Hide file tree
Changes from 5 commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
008020a
add full size test NA12878
ggabernet Jun 24, 2022
7f4bd0c
update changelog
ggabernet Jun 24, 2022
d54750e
add tools
ggabernet Jun 24, 2022
2c8ad47
Merge branch 'dev' into full-tests
ggabernet Jun 24, 2022
f015391
add tools
ggabernet Jun 27, 2022
bae2431
change tools
ggabernet Jun 28, 2022
bc4bebe
Merge branch 'dev' into full-tests
ggabernet Jun 28, 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 @@ -33,6 +33,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [#594](https://github.com/nf-core/sarek/pull/594) - Add parameter `--save_output_as_bam` to allow output of result files in BAM format
- [#600](https://github.com/nf-core/sarek/pull/600) - Added description for UMI related params in schema
- [#597](https://github.com/nf-core/sarek/pull/597) - Added tiddit for tumor variant calling
- [#604](https://github.com/nf-core/sarek/pull/604) - Added full size tests WGS 30x NA12878

### Changed

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 = "${projectDir}/tests/csv/3.0/test_full_data.csv"
input = '${projectDir}/tests/csv/3.0/test_full_data.csv'

wes = true

// Ignore `--input` as otherwise the parameter validation will throw an error
// Other params
tools = 'strelka,freebayes,haplotypecaller,deepvariant,manta,tiddit,ascat,snpeff,vep'
Copy link
Contributor

Choose a reason for hiding this comment

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

ASCAT only works for paired samples at the moment., cnvkit however is also implemented for germline only mode

Copy link
Member

Choose a reason for hiding this comment

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

Do we really want to do annotation? The containers are huge

Copy link
Member Author

Choose a reason for hiding this comment

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

well it's a full test so it shouldn't matter much, but maybe just VEP for now then

genome = 'GATK.GRCh38'
vep_cache_version = 105
schema_ignore_params = 'genomes'
}
2 changes: 1 addition & 1 deletion tests/csv/3.0/test_full_data.csv
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,2 +1,2 @@
patient,status,sample,lane,fastq_1,fastq_2
HG002,0,HG002,1,s3://giab/data/AshkenazimTrio/HG002_NA24385_son/NIST_Illumina_2x250bps/reads/D1_S1_L001_R1_001.fastq.gz,s3://giab/data/AshkenazimTrio/HG002_NA24385_son/NIST_Illumina_2x250bps/reads/D1_S1_L001_R2_001.fastq.gz
NA12878,0,NA12878,1,s3://nf-core-awsmegatests/sarek/input/NA12878_1.merged.fastq.gz,s3://nf-core-awsmegatests/sarek/input/NA12878_2.merged.fastq.gz