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artic-network
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fieldbioinformatics
The ARTIC field bioinformatics pipeline
MIT License
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update envs, tests and add argparse to margin_cons.py
#23
Closed
will-rowe
closed
4 years ago
will-rowe
commented
4 years ago
This PR:
tidies up the conda envs
removes pip installs from conda (artic-porechop now via conda)
consolidates medaka and nanopolish envs into a single env
adds muscle for upstream pipeline change
now nanopolish 0.12.5 is in conda, update Travis to also test against OSX
adds argparse to
margin_cons.py
so that the CLI can be tested easily
updates README with a brief intro and some installation details
adds command execution time to the minion log (as an additional tab-separated column)
adds documentation for tests
adds variant validation tests
adds data download option for tests
updates
pipeline.py
with some minor fixes:
removes duplicated guppyplex cmd
renames
filter.py
to
filter_reads.py
to avoid function overwrite
updated minion help text
adds more documentation
This PR:
margin_cons.py
so that the CLI can be tested easilypipeline.py
with some minor fixes:filter.py
tofilter_reads.py
to avoid function overwrite