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Improved workflows-as-applications: tips and tricks for building applications on top of snakemake

ivory.idyll.org · published 5 August 2020

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Link
Host
https://github.com/metagenome-atlas/atlas
github.com
https://dib-lab.github.io/2020-workflows-paper/
dib-lab.github.io
https://www.biorxiv.org/content/10.1101/2020.06.30.178673v1
biorxiv.org
https://github.com/spacegraphcats/spacegraphcats/tree/2e82cc46cd25e71a1158d641760a11fdb940583d/spacegraphcats/search
github.com
https://github.com/dib-lab/dammit
github.com
https://github.com/dahak-metagenomics/dahak
github.com
https://github.com/spacegraphcats/spacegraphcats
github.com
https://github.com/dib-lab/elvers
github.com
https://github.com/dib-lab/charcoal
github.com
https://github.com/spacegraphcats/spacegraphcats/blob/2e82cc46cd25e71a1158d641760a11fdb940583d/spacegraphcats/conf/Snakefile
github.com
https://github.com/spacegraphcats/spacegraphcats/blob/2e82cc46cd25e71a1158d641760a11fdb940583d/spacegraphcats/__main__.py
github.com
https://github.com/spacegraphcats/spacegraphcats/blob/master/doc/running-spacegraphcats.md
github.com
https://github.com/spacegraphcats/spacegraphcats/blob/2e82cc46cd25e71a1158d641760a11fdb940583d/spacegraphcats/conf/twofoo.yaml
github.com
https://github.com/dib-lab/charcoal/blob/dfc18387a7f88abb77941a5c0528b924bc43b237/charcoal/conf/system.conf
github.com
https://github.com/dib-lab/charcoal/blob/dfc18387a7f88abb77941a5c0528b924bc43b237/charcoal/Snakefile
github.com
https://github.com/dib-lab/charcoal/blob/dfc18387a7f88abb77941a5c0528b924bc43b237/charcoal/__main__.py
github.com
https://snakemake.readthedocs.io/en/v5.1.4/executable.html
snakemake.readthedocs.io
https://github.com/spacegraphcats/spacegraphcats/blob/d049876a2f4c452fe9ea42a0db70b7c2f3b6112d/spacegraphcats/click.py
github.com
https://github.com/spacegraphcats/spacegraphcats/blob/2e82cc46cd25e71a1158d641760a11fdb940583d/spacegraphcats/search/test_workflow.py
github.com
https://github.com/spacegraphcats/spacegraphcats/blob/d049876a2f4c452fe9ea42a0db70b7c2f3b6112d/spacegraphcats/test_snakemake.py
github.com
https://snakemake.readthedocs.io/en/stable/snakefiles/configuration.html
snakemake.readthedocs.io
https://github.com/dib-lab/2020-ibd/blob/50404a7cfcd41ce1ed809ba8aaddb1939e279e8e/Snakefile
github.com
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