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h3abionet / HPCBio-Refgraph_pipeline

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Containerization of tools #5

Closed cjfields closed 3 years ago

cjfields commented 4 years ago

@yuantianhpc when you have time, we'll need a list of tools here that can be containerized. Can use the task list (check box) in the above so anyone working on this can help generate them or point to new ones.

cjfields commented 4 years ago

Hi @yuantianhpc can you add a list of tools that we can prioritize for containerization here? Off the top of my head I can think of:

Are there others?

yuantianhpc commented 4 years ago

Hi @yuantianhpc can you add a list of tools that we can prioritize for containerization here? Off the top of my head I can think of:

  • samtools
  • FASTQC
  • MEGAHIT
  • Kraken2
  • MaSurCA

Are there others?

The ones you listed above contain all in the current pipeline. Thank you! We may add trim tools to it, Trimmomatic and fastp.

cjfields commented 3 years ago

Now added to the Hackathon (along with some additional tools):

https://docs.google.com/spreadsheets/d/1y3yj1TiFjra5D2Pvmay2IeU-sfOkZmN6b_POEPtEEuw/edit?usp=sharing