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TrinityCTAT / CTAT-VirusIntegrationFinder

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Pass files to tasks instead of genome lib dir #12

Closed joshua-gould closed 3 years ago

brianjohnhaas commented 3 years ago

I think there are processes in ctat-VIF that use the genome lib in order to extract the gene annotations (or may in the future). The ctat genome lib is at the heart of many of the ctat-tools, and so I'm not super psyched about removing the genome lib parameter. Do we really need to do this for some reason?

joshua-gould commented 3 years ago

The genome lib parameter remains at the top level, but passes the needed files within the genome lib to each task.

On Mon, Mar 22, 2021 at 7:02 PM Brian Haas @.***> wrote:

I think there are processes in ctat-VIF that use the genome lib in order to extract the gene annotations (or may in the future). The ctat genome lib is at the heart of many of the ctat-tools, and so I'm not super psyched about removing the genome lib parameter. Do we really need to do this for some reason?

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brianjohnhaas commented 3 years ago

ah! ok, that makes sense. thanks!

On Mon, Mar 22, 2021 at 7:06 PM Joshua Gould @.***> wrote:

The genome lib parameter remains at the top level, but passes the needed files within the genome lib to each task.

On Mon, Mar 22, 2021 at 7:02 PM Brian Haas @.***> wrote:

I think there are processes in ctat-VIF that use the genome lib in order to extract the gene annotations (or may in the future). The ctat genome lib is at the heart of many of the ctat-tools, and so I'm not super psyched about removing the genome lib parameter. Do we really need to do this for some reason?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/broadinstitute/CTAT-VirusIntegrationFinder/pull/12#issuecomment-804453131, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABZRKXY3MGRH2IDMAV7R5KLTE7ENZANCNFSM4ZUAZG3A .

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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas