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Add support for custom conda channels #3435

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merged 2 commits into from
Nov 25, 2022
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This PR adds the support for custom conda channels.

The channels can be specified in the nextflow config e.g.

conda {
  channels = ['bioconda','defaults']
}

They are used when creating the Conda environment via punctual packages specified via the conda directive e.g.

process foo {
  conda 'samtools'
} 

Note, custom channels are ignored when the conda directive specified a Conda recipe yaml file

Signed-off-by: Paolo Di Tommaso paolo.ditommaso@gmail.com

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
@pditommaso pditommaso requested a review from jordeu November 25, 2022 11:27
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
@pditommaso pditommaso merged commit 0884e80 into master Nov 25, 2022
@pditommaso pditommaso deleted the conda-custom-channels branch November 25, 2022 16:07
@abhi18av abhi18av linked an issue Nov 29, 2022 that may be closed by this pull request
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Add support for custom channels to Conda
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