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nf-core / ampliseq

Amplicon sequencing analysis workflow using DADA2 and QIIME2
https://nf-co.re/ampliseq
MIT License
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Please upload the environment.yml file #499

Closed karnival21 closed 1 year ago

karnival21 commented 2 years ago

Description of feature

I am trying to use the environment.yml file to create a new conda environment, but I can't find it. Can you upload the environment.yml file, please?

d4straub commented 2 years ago

There is no environment.yml any more. The environment.yml was last used in version 1.2.0, and I cannot recommend using that version. Since version 2.0.0 the pipeline is written in nextflow DSL2 syntax (instead of DSL2, which used the environment.yml). Now the pipeline uses its own container/conda environment for each process. You can run the current pipeline version pipeline with nextflow run nf-core/ampliseq -r 2.4.0 -profile test,conda --outdir results_test --skip_qiime, the last parameter will omit any downstream analysis with qiime2 because that doesnt support a straight forward conda environment. I'd recommend using one of the container programs like docker or singularity though.

d4straub commented 1 year ago

I am closing this but please feel free to open another issue when coming across a problem.