TESTS.md

Testing Sarek

For testing purpose we provide Sarek-data, a repository with test data and corresponding reference files.

One simple bash script is available, which will pull the Sarek-data repository and perform all the tests:

• scripts/test.sh

Such tests are used in our Continuous Integration with Travis. You can perform the same tests to familiarize yourself with the workflow.

Testing with Singularity

For testing with Docker, just replace singularity with docker in every occurence.

# Dowload Sarek and the test data
git clone --recursive https://github.com/SciLifeLab/Sarek Sarek-test
cd Sarek-test

# Build the references for the test data
nextflow run build.nf --outDir References/smallGRCh37 \
  --refDir Sarek-data/reference --tag latest \
  -profile singularity

# Testing --sampleDir as input for Germline
nextflow run main.nf --sampleDir Sarek-data/testdata/manta/normal \
  --step mapping --genome smallGRCh37 --genome_base References/smallGRCh37 \
  --tag latest -profile singularity

# Testing to restart from `recalibrate`
nextflow run main.nf --step recalibrate \
  --genome smallGRCh37 --genome_base References/smallGRCh37 \
  --tag latest -profile singularity

# Testing germline variant calling
nextflow run germlineVC.nf --genome smallGRCh37 \
  --genome_base References/smallGRCh37 --tools HaplotypeCaller,Manta,Strelka \
  --tag latest -profile singularity

# Testing generating report
nextflow run runMultiQC.nf -profile singularity

# Removing test data before new tests
rm -rf Preprocessing Reports VariantCalling

# Testing --sample as input for Somatic
nextflow run main.nf --sample Sarek-data/testdata/tsv/tiny-manta.tsv \
  --step mapping --genome smallGRCh37 --genome_base References/smallGRCh37 \
  --tag latest -profile singularity

# Testing germline variant calling
nextflow run germlineVC.nf --genome smallGRCh37 \
  --genome_base References/smallGRCh37 --tools HaplotypeCaller,Manta,Strelka \
  --tag latest -profile singularity

# Testing somatic variant calling
nextflow run somaticVC.nf --genome smallGRCh37 \
  --genome_base References/smallGRCh37 --tools Manta,Strelka,FreeBayes,MuTect2 \
  --tag latest -profile singularity

# Testing somatic variant calling following Strelka2 Best Practices
nextflow run somaticVC.nf --genome smallGRCh37 \
  --genome_base References/smallGRCh37 --tools Manta,Strelka,FreeBayes,MuTect2 \
  --strelkaBP --tag latest -profile singularity

# Testing annotation
nextflow run annotate.nf --tools snpEFF,VEP \
  --annotateVCF VariantCalling/StrelkaBP/Strelka_9876T_vs_1234N_somatic_indels.vcf.gz \
  -profile singularity

# Testing generating report
nextflow run runMultiQC.nf -profile singularity

Testing on a secure cluster

On a secure cluster as bianca, with no internet access, you will need to download and transfer Sarek and the test data first.

Follow the installation guide for bianca.

And then start the test at the Build the references for the test data step.

Usage

Four optional arguments are supported:

• -g || --genome: Choose the genome reference version (overwrite configuration files and profiles)
• -p || --profile: Choose which profile to test. These options should work on a personal computer:
  • docker test using Docker containers
  • singularity (default) test using Singularity containers
• -s || --sample: Use to change the test sample (default=Sarek-data/testdata/tsv/tiny.tsv)
• -t || --test:
• GERMLINE: test mapping, recalibrate and Variant Calling with HaplotypeCaller
• SOMATIC: test mapping and Variant Calling with FreeBayes, HaplotypeCaller, MuTect2, Strelka and Manta
• ANNOTATESNPEFF: test annotation using snpEFF
• ANNOTATEVEP: test annotation using VEP
• BUILDCONTAINERS: test building all containers except snpeffgrch37, snpeffgrch38, vepgrch37 and vepgrch38
• ALL: test all the previous tests (default)

# Will perform all tests using Singularity
./scripts/test.sh
# Will perform all tests using Docker
./scripts/test.sh -p docker
# Will perform `STEP` tests using Singularity
./scripts/test.sh -t `STEP`
# Will perform `STEP` tests using Singularity with GRCh37 genome
./scripts/test.sh -t `STEP` -g GRCh37
# Will perform all tests using Singularity on manta test data
./scripts/test.sh -s Sarek-data/testdata/tsv/tiny-manta.tsv