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biocore / micronota

annotation pipeline for microbial genomes and metagenomes
BSD 3-Clause "New" or "Revised" License
18 stars 10 forks source link

use snakemake and IntervalMetadata #78

Closed RNAer closed 7 years ago

RNAer commented 7 years ago

it depends on the branch of scikit-bio: https://github.com/rnaer/scikit-bio/tree/micronota, where the genbank parser and gff3 parser is waiting to be merged to skbio.

coveralls commented 7 years ago

Coverage Status

Coverage decreased (-21.6%) to 57.312% when pulling 46e5ecb16aba538aef9a40f470684f8b6fc60e5d on RNAer:snakemake into c1b688b4ba46d73285abb87cc07e365c90f98043 on biocore:master.

mortonjt commented 7 years ago

damn - there are no tests here ...

We can't have this sort of test coverage on the master branch. Let's create a developer branch - so we can more easily sort out the outstanding tasks ...

RNAer commented 7 years ago

it is just because of the snakemake files. The coverage will increase when more code comes in.

mortonjt commented 7 years ago

right - which is why we should be pushing this into a development branch, not the master branch.

We did this strategy with Emperor. This won't slow down development.

coveralls commented 7 years ago

Coverage Status

Coverage decreased (-21.6%) to 57.312% when pulling 46e5ecb16aba538aef9a40f470684f8b6fc60e5d on RNAer:snakemake into c1b688b4ba46d73285abb87cc07e365c90f98043 on biocore:master.