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tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
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Can I start the pipeline at the forth step 'Annotation' #213

Closed tigerxu closed 5 years ago

tigerxu commented 5 years ago

Hi,

I have assembled contigs for the collected genomes. I'm wondering if I can start the nullarbor pipeline at the forth step 'Annotation'?

Thank you very much!

Zhuofei

tseemann commented 5 years ago

Yes, you can copy the contigs into their SAMPLEID/contigs.fa location and the Makefile should just use them instead of assembling them again.

The other way is to edit nullarbor.conf and the [prefill] section.

Please copy the files though, do not move them. As there is chance things will go wrong and they will be overwritten.

tigerxu commented 5 years ago

Many thanks for your quick reply!

On Wed, 30 Jan 2019 at 08:53, Torsten Seemann notifications@github.com wrote:

Yes, you can copy the contigs into their SAMPLEID/contigs.fa location and the Makefile should just use them instead of assembling them again.

The other way is to edit nullarbor.conf and the [prefill] section.

Please copy the files though, do not move them. As there is chance things will go wrong and they will be overwritten.

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