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Simple conda requirements and docker image for nextflow pipeline #150

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chasemc opened this issue Apr 27, 2021 · 2 comments · Fixed by #157
Closed

Simple conda requirements and docker image for nextflow pipeline #150

chasemc opened this issue Apr 27, 2021 · 2 comments · Fixed by #157
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nextflow Nextflow related issues/code question Further information is requested

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@chasemc
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chasemc commented Apr 27, 2021

First- I have most all the nextflow stuff in ~/Autometa/nextflow now, with only a false-config in the main directory ~/Autometa/ so that someone can pull the pipeline directly from nextflow.

I was thinking of making another, simple requirements.txt and dockerfile within the/Autometa/nextflow directory that are specific for running the nextflow pipeline. They would be simple: likely only including nf-core, nextflow, aspera.

The main reason is nextflow and/or nf-core are required to be installed in order for the pipeline to run but I don't think should be in the mostly-python oriented https://github.com/KwanLab/Autometa/blob/dev/requirements.txt

Thoughts?

@chasemc chasemc added question Further information is requested nextflow Nextflow related issues/code labels Apr 27, 2021
@evanroyrees
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This may be easier to review under a pull request with your code changes. This way the context of your changes and the discussion are all in one place and up to date.

@chasemc chasemc linked a pull request Apr 28, 2021 that will close this issue
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chasemc commented Sep 28, 2021

Fixed by #157

@chasemc chasemc closed this as completed Sep 28, 2021
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