.dockerignore
.git_archival.txt
.gitattributes
.gitignore
Dockerfile
LICENSE
MANIFEST.in
README.md
documentation.md
pyproject.toml
setup.cfg
setup.py
.github/logo.jpg
.github/workflows/joss.yml
.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/requires.txt
acanthophis.egg-info/top_level.txt
acanthophis/template/config.yml
acanthophis/template/environment.yml
acanthophis/template/rawdata/adapters.txt
acanthophis/template/rawdata/nextera.txt
acanthophis/template/workflow/Snakefile
acanthophis/template/workflow/config.schema.yml
acanthophis/template/workflow/profiles/cobra.mpcdf/README.md
acanthophis/template/workflow/profiles/cobra.mpcdf/cluster.yml
acanthophis/template/workflow/profiles/cobra.mpcdf/config.yaml
acanthophis/template/workflow/profiles/cobra.mpcdf/jobscript.sh
acanthophis/template/workflow/profiles/cobra.mpcdf/jobstatus
acanthophis/template/workflow/profiles/cobra.mpcdf/jobsubmit
acanthophis/template/workflow/profiles/cobra.mpcdf/resources.yml
acanthophis/template/workflow/profiles/cobra.mpcdf/submit.sh
acanthophis/template/workflow/profiles/ebio-cluster/README.md
acanthophis/template/workflow/profiles/ebio-cluster/cluster.yml
acanthophis/template/workflow/profiles/ebio-cluster/config.yaml
acanthophis/template/workflow/profiles/ebio-cluster/jobscript.sh
acanthophis/template/workflow/profiles/ebio-cluster/jobstatus
acanthophis/template/workflow/profiles/ebio-cluster/jobsubmit
acanthophis/template/workflow/profiles/ebio-cluster/resources.yml
acanthophis/template/workflow/profiles/ebio-cluster/run.job
acanthophis/template/workflow/profiles/ebio-cluster/submit.sh
acanthophis/template/workflow/profiles/ebio-cluster-semilocal/README.md
acanthophis/template/workflow/profiles/ebio-cluster-semilocal/cluster.yml
acanthophis/template/workflow/profiles/ebio-cluster-semilocal/config.yaml
acanthophis/template/workflow/profiles/ebio-cluster-semilocal/jobscript.sh
acanthophis/template/workflow/profiles/ebio-cluster-semilocal/jobstatus
acanthophis/template/workflow/profiles/ebio-cluster-semilocal/jobsubmit
acanthophis/template/workflow/profiles/ebio-cluster-semilocal/resources.yml
acanthophis/template/workflow/profiles/ebio-cluster-semilocal/run.job
acanthophis/template/workflow/profiles/ebio-cluster-semilocal/submit.sh
acanthophis/template/workflow/profiles/gadi.nci.org.au/README.md
acanthophis/template/workflow/profiles/gadi.nci.org.au/cluster.yml
acanthophis/template/workflow/profiles/gadi.nci.org.au/config.yaml
acanthophis/template/workflow/profiles/gadi.nci.org.au/jobscript.sh
acanthophis/template/workflow/profiles/gadi.nci.org.au/jobstatus
acanthophis/template/workflow/profiles/gadi.nci.org.au/jobsubmit
acanthophis/template/workflow/profiles/gadi.nci.org.au/run.job
acanthophis/template/workflow/profiles/gadi.nci.org.au/submit.sh
acanthophis/template/workflow/profiles/local/config.yaml
acanthophis/template/workflow/profiles/local/resources.yml
acanthophis/template/workflow/rules/align.rules
acanthophis/template/workflow/rules/base.rules
acanthophis/template/workflow/rules/deepvariant.rules
acanthophis/template/workflow/rules/denovo.rules
acanthophis/template/workflow/rules/metagenome.rules
acanthophis/template/workflow/rules/reads.rules
acanthophis/template/workflow/rules/sampleset.rules
acanthophis/template/workflow/rules/taxonid.rules
acanthophis/template/workflow/rules/varcall.rules
acanthophis/template/workflow/rules/variantannotation.rules
acanthophis/template/workflow/rules/envs/align.yml
acanthophis/template/workflow/rules/envs/bakery.yml
acanthophis/template/workflow/rules/envs/centrifuge.yml
acanthophis/template/workflow/rules/envs/deepvariant.yml
acanthophis/template/workflow/rules/envs/diamond.yml
acanthophis/template/workflow/rules/envs/glnexus.yml
acanthophis/template/workflow/rules/envs/global.yml
acanthophis/template/workflow/rules/envs/idxcov.yml
acanthophis/template/workflow/rules/envs/kaiju.yml
acanthophis/template/workflow/rules/envs/kraken.yml
acanthophis/template/workflow/rules/envs/kwip.yml
acanthophis/template/workflow/rules/envs/mash.yml
acanthophis/template/workflow/rules/envs/megahit.yml
acanthophis/template/workflow/rules/envs/qcstats.yml
acanthophis/template/workflow/rules/envs/qualimap.yml
acanthophis/template/workflow/rules/envs/reads.yml
acanthophis/template/workflow/rules/envs/snpeff.yml
acanthophis/template/workflow/rules/envs/sra.yml
acanthophis/template/workflow/rules/envs/varcall.yml
paper/.gitignore
paper/paper.bib
paper/paper.md
tests/.config_quick.yml
tests/.gitignore
tests/README.md
tests/Snakefile.generate-rawdata
tests/environment-setup.yml
tests/setup.sh
tests/test.sh
tests/.snakemake/nobackup
tests/rawdata/nobackup
tests/rawdata/lambda/centrifuge-map.txt
tests/rawdata/lambda/lambda.fasta
tests/rawdata/lambda/lambda.gb
tests/rawdata/lambda/lambda.gff
tests/rawdata/lambda/lambda.gtf