.editorconfig
.gitignore
LICENSE
MANIFEST.in
Makefile
README.md
setup.cfg
setup.py
examples/resequencing/README.md
examples/resequencing/download_urls.txt
examples/resequencing/step1-prepare.bash
examples/resequencing/step2-submit_reference.bash
examples/resequencing/step3-submit_sample.bash
examples/resequencing/data/reference/hs37d5/hs37d5.gpipe.yml
examples/resequencing/data/reference/hs37d5/hs37d5.reference.yml
examples/resequencing/data/sample/HG005/HG005.gpipe.yml
examples/resequencing/workflow/00-reference.workflow.py
examples/resequencing/workflow/11-single_sample.workflow.py
examples/resequencing/workflow/common.py
examples/resequencing/workflow/libs/fasta.py
examples/resequencing/workflow/libs/reference.py
examples/resequencing/workflow/modulefiles.template/bcftools-1.7
examples/resequencing/workflow/modulefiles.template/bwa-0.7.12
examples/resequencing/workflow/modulefiles.template/fastqc-0.11.2
examples/resequencing/workflow/modulefiles.template/gatk-3.8-0
examples/resequencing/workflow/modulefiles.template/java-1.8.0_162
examples/resequencing/workflow/modulefiles.template/picard-2.10.6
examples/resequencing/workflow/modulefiles.template/samtools-1.7
examples/resequencing/workflow/scripts/x-generate_interval_list_from_dict.py
examples/resequencing/workflow/scripts/x-mask_fasta.py
examples/resequencing/workflow/scripts/x-shift_fasta.py
examples/resequencing/workflow/scripts/x-verify_par_masked.py
gpipe/__init__.py
gpipe/cli.py
gpipe/dsl.py
gpipe.egg-info/PKG-INFO
gpipe.egg-info/SOURCES.txt
gpipe.egg-info/dependency_links.txt
gpipe.egg-info/entry_points.txt
gpipe.egg-info/requires.txt
gpipe.egg-info/top_level.txt
gpipe/commands/__init__.py
gpipe/commands/cancel.py
gpipe/commands/clean.py
gpipe/commands/graph.py
gpipe/commands/run.py
gpipe/commands/version.py
gpipe/utils/__init__.py
gpipe/utils/click_support.py
gpipe/utils/config.py
gpipe/utils/container.py
gpipe/utils/log.py
gpipe/utils/module.py
gpipe/utils/path.py
gpipe/utils/pyobject.py
gpipe/utils/template.py
gpipe/workflow/__init__.py
gpipe/workflow/execution.py
gpipe/workflow/model.py
gpipe/workflow/sge/array_task_script_template.sh.j2
gpipe/workflow/sge/single_task_script_template.sh.j2