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# content of pytest.ini
[pytest]
markers =
cancer: cancer variant calling pipeline
cancermulti: cancer variant calling pipeline with multiple callers
cancerpanel: cancer variant calling pipeline on panels
cancerprecall: cancer pipeline with pre-called variants
combo: not sure what this test is for
devel: test for unsupported features still in development
ensemble: test variant calling with multiple callers
fastrnaseq: test fast RNA-seq pipeline
hisat2: test functionality of hisat2 aligner
hla: test HLA typing
install_required: installation of bcbio is required for this test
joint: test joint calling
rnaseq: RNA-seq pipeline
rnaseq_standard: test standard RNA-seq calling pipeline
rnaseq_vc: test RNA-seq variant calling
S3: test S3 integration
scrnaseq: test single-cell RNA-seq
singleend: test single-end functionality
speed1: fast suite of tests
speed2: slower suite of tests
speed3: slowest and most complete suite of tests
srnaseq: test small RNA-seq pipeline
srnaseq_bowtie: test small RNA-seq pipeline using bowtie as the aligner
srnaseq_star: test small RNA-seq pipeline using STAR as the aligner
stranded: test stranded RNA-seq run
template: test automatic templating step
tophat: test RNA-seq pipeline using tophat
umibarcode: test UMI pipelines
docker: test docker pipelines
multicore: test parallelization via multicore
ipython: test parallelization via IPython
cwl: test CWL (Common Workflow Language) pipelines
somatic: test somatic calling pipeline
docker_somatic: test docker-based somatic variant calling
docker_joint: test docker-based joint calling
docker_rnaseq: test docker-based RNA-seq pipeline
docker_multicore: test multicore parallelization with docker
docker_ipython: test IPython parallelization in docker
cwl_docker: test CWL with docker
cwl_docker_somatic: test the somatic pipeline using CWL and docker
cwl_docker_joint: test the joint calling pipeline using CWL and docker
cwl_docker_rnaseq: test the RNA-seq pipeline using CWL and docker
cwl_local: test CWL using a local runner
cwl_arvados: test CWL running on Arvados
fusion: test RNA-seq fusion calling functionaltiy
star: test RNA-seq using STAR
explant: test explant disambiguation
chipseq: test ChIP-seq pipeline
ericscript: test Ericscript integration
atacseq: test ATAC-seq pipeline
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