def main(order):
    piper = PiperFactory.create_piper(order)
    play_pipe(piper)


def play_pipe(piper):
    piper.pipe_stdin()
    cmd = piper.render_user_cmd(order=piper.order,)
    piper.run_user_script(cmd)
    piper.collect_output_files()
    piper.upload_output_files()
    piper.teardown()

├── seqpiper
│   ├── base
│   ├── bam
│   ├── vcf
│   │   ├── base.py
│   │ 
│   ├── main.py
│
├── tests
    ├── phasing.sh
    ├── imputation.sh

class VcfPiperBase(PiperAbstractFactory):
    def pipe_stdin(self):
        some_vcf_function()

class PiperAbstractFactory(object):
    @abstractmethod
    def stdin(self):
        pass
  
    def render_user_cmd(self):
        some code
    
    def run_user_script(self):
        some code
    
    def collect_output_files(self):
        some code
    
    def upload_output_files(self):
        some code
    
    def teardown(self):
        some code

import sys
import traceback

sys.path.append('/usr/local/seqslab/SeqPiper')

from script.library.GatkWrapper import ApplyRecalibration
from script.common.base import SeqPiperBase
from script.common.order import JobOrder
from script.common.exception import SeqPiperEmptyVariantFile

import sys
import traceback

from script.library.GatkWrapper import ApplyRecalibration
from script.common.base import SeqPiperBase
from script.common.order import JobOrder
from script.common.exception import SeqPiperEmptyVariantFile

sys.path.append('/usr/local/seqslab/SeqPiper')

setup(
    name="seqpiper",
    version="0.0.1",
    long_description=readme,
    long_description_content_type="text/markdown",
    url="",
    author="",
    author_email="",
    license="",
    install_requires=[],
    keywords="bioinformatics, seqpiper",
    packages=find_packages(),
)

python3 setup.py install

import sys
import traceback

from script.library.GatkWrapper import ApplyRecalibration
from script.common.base import SeqPiperBase
from script.common.order import JobOrder
from script.common.exception import SeqPiperEmptyVariantFile

/opt/bitnami/spark/bin/spark-submit \
  --class net.vartotal.piper.cli.PiperMain \
  --driver-cores 1 \
  --driver-memory 1g \
  --executor-cores 1 \
  --executor-memory 10g \
  --conf "spark.dynamicAllocation.enabled=false" \
  --conf "spark.executor.extraJavaOptions=-XX:+UseG1GC" \
  --conf "spark.serializer=org.apache.spark.serializer.KryoSerializer" \
  --conf "spark.kryo.registrator=net.vartotal.piper.serialization.ADAMKryoRegistrator" \
  --conf "spark.executor.memoryOverhead=14g" \
  --conf "spark.speculation=false" \
  /usr/local/seqslab/SeqPiper/target/piper-2.1.0.jar vcf \
  --reference-version 38 \
  --reference-system GRCH \
  --piper-script fixtures.scripts.no_stdout \
  -i 0=/usr/local/seqslab/SeqPiper/fixtures/vcf/ \
  --samplePath /usr/local/seqslab/SeqPiper/fixtures/vcf/ \
  --vcf-output-path vcf_gz_folder \
  --partition-bed-path /usr/local/seqslab/SeqPiper/fixtures/bed/38/chromosomes

├── seqpiper
│   ├── base
│   ├── bam
│   ├── vcf
│   │   ├── base.py
│   │ 
│   ├── main.py
│
├── tests
    ├── phasing.sh
    ├── imputation.sh