Curtis dev

[kapsakcj]

Merge to include the new shovill v1.0.4 dockerfile. Will add to docker hub soon.

Beware I've only tested the image/container on two salmonella isolates but it seemed to run with no issues. I haven't tried anything other than the default options.

I got some great messages at the end, too!

[shovill] Using genome graph file 'spades/assembly_graph_with_scaffolds.gfa' => 'contigs.gfa'
[shovill] Walltime used: 8 min 40 sec
[shovill] Results in: /data/shovill-test
[shovill] Final assembly graph: /data/shovill-test/contigs.gfa
[shovill] Final assembly contigs: /data/shovill-test/contigs.fa
[shovill] It contains 115 (min=112) contigs totalling 4876808 bp.
[shovill] A shovel will move more dirt than a spade.
[shovill] Done.

[shovill] Walltime used: 8 min 30 sec
[shovill] Results in: /data/shovill-PNUSAS060846
[shovill] Final assembly graph: /data/shovill-PNUSAS060846/contigs.gfa
[shovill] Final assembly contigs: /data/shovill-PNUSAS060846/contigs.fa
[shovill] It contains 129 (min=114) contigs totalling 4974584 bp.
[shovill] Wishing you a life free of misassemblies.
[shovill] Done.

[kapsakcj]

Anything I add or edit, I'll do in the curtis-dev branch and create a pull request so that I'm not pushing commits to the master branch, causing docker-hub auto builds to kick off every time I commit.