.dockerignore
.git_archival.txt
.gitattributes
.gitignore
Dockerfile
LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
setup.py
.github/logo.jpg
.github/workflows/python-publish.yml
.github/workflows/run-snakemake.yml
acanthophis/__init__.py
acanthophis/_version.py
acanthophis/cmd.py
acanthophis.egg-info/PKG-INFO
acanthophis.egg-info/SOURCES.txt
acanthophis.egg-info/dependency_links.txt
acanthophis.egg-info/entry_points.txt
acanthophis.egg-info/top_level.txt
acanthophis/envs/abra2.yml
acanthophis/envs/align.yml
acanthophis/envs/global.yml
acanthophis/envs/kraken.yml
acanthophis/envs/qcstats.yml
acanthophis/envs/qualimap.yml
acanthophis/envs/reads.yml
acanthophis/envs/snpeff.yml
acanthophis/envs/varcall.yml
acanthophis/profiles/ebio-cluster/README.md
acanthophis/profiles/ebio-cluster/cluster.yml
acanthophis/profiles/ebio-cluster/config.yaml
acanthophis/profiles/ebio-cluster/jobscript.sh
acanthophis/profiles/ebio-cluster/jobstatus
acanthophis/profiles/ebio-cluster/jobsubmit
acanthophis/profiles/ebio-cluster/run.job
acanthophis/profiles/ebio-cluster/submit.sh
acanthophis/profiles/gadi.nci.org.au/README.md
acanthophis/profiles/gadi.nci.org.au/cluster.yml
acanthophis/profiles/gadi.nci.org.au/config.yaml
acanthophis/profiles/gadi.nci.org.au/jobscript.sh
acanthophis/profiles/gadi.nci.org.au/jobstatus
acanthophis/profiles/gadi.nci.org.au/jobsubmit
acanthophis/profiles/gadi.nci.org.au/run.job
acanthophis/profiles/gadi.nci.org.au/submit.sh
acanthophis/rules/align.rules
acanthophis/rules/base.rules
acanthophis/rules/denovo.rules
acanthophis/rules/gatk.rules
acanthophis/rules/kraken.rules
acanthophis/rules/multiqc.rules
acanthophis/rules/qualimap.rules
acanthophis/rules/reads.rules
acanthophis/rules/varcall.rules
acanthophis/rules/variantannotation.rules
acanthophis/template/Snakefile
acanthophis/template/config.yml
acanthophis/template/environment.yml
acanthophis/template/rawdata/adapters.txt
example/.gitignore
example/README.md
example/Snakefile
example/Snakefile.generate-rawdata
example/config.yml
example/environment_demo.yml
example/setup.sh
example/lambda/lambda.fasta
example/lambda/lambda.gb
example/lambda/lambda.gff
example/lambda/lambda.gtf