Yet Another Pipeline System (YAPS) 2 (COSMOS2-based)

A work in progress. Not really ready for prime time. This is a pure idea experiment and code may be abandoned in the future.

yaps is based on ruffus. This repository, yaps2, is based on a tweaked COSMOS2.

Example execution

yaps2 postvqsr --workspace=/path/to/workspace/name/test-pipeline --input-vcfs=inputs.txt --project-name="test-pipeline" --timeout=300 --log-level=INFO

Deployment

pip install --no-cache-dir --process-dependency-links git+https://github.com/indraniel/yaps2.git
# pygraphviz needs some extra install help
pip install pygraphviz --install-option="--include-path=/usr/include/graphviz" --install-option="--library-path=/usr/lib/graphviz/" --force-reinstall --upgrade

Development

git clone https://github.com/indraniel/yaps2.git
cd yaps2
virtualenv venv
source venv/bin/activate
pip install --no-cache-dir --process-dependency-links -e .
# pygraphviz needs some extra install help
pip install pygraphviz --install-option="--include-path=/usr/include/graphviz" --install-option="--library-path=/usr/lib/graphviz/" --force-reinstall --upgrade
# < do development work >
 
# test
yaps2 postvqsr --workspace=/path/to/workspace/name/test-pipeline --input-vcfs=inputs.txt --project-name="test-pipeline" --timeout=300 --log-level=INFO

# clean up dev workspace
make clean

Misc. Notes

BIO-1984 is the "grandfather" issue for most of these pipelines. See yaps2 --help and/or yaps <pipeline> --help for more information on the available commands/pipelines and options.

postvqsr pipeline

• --input-vcfs is a file containing a tab-separated list of *.vcf.gz files in <CHROM>\t<VCF.GZ FILE> format
• Example Usage (see BIO-1984 -- BIO-1984/bin/run-pipeline.sh)

Mendelian Error Rate mie pipeline

• Example Usage (see BIO-2000 -- BIO-2000/bin/1-run-pipeline.sh)

Principal Component Analysis pca pipeline

• Example Usage (see BIO-2020 -- BIO-2020/bin/1-run-pipeline.sh`)

Build38 realignment b38 pipeline

• Example Usage (see BIO-2078 -- BIO-2078/bin/19-run-speedseq-realign-pipeline.sh)