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nf-core/sarek pipeline : adding genome index in config file

Hello all,

When i try nf-core/sarek for the first time i have faced few issues that i share below,

  1. The pipeline stopped after few minutes and showing " Process requirement exceeds available memory :required 36 GB ;available 29.5 GB" - Error while createsequencedictionary

So, I've add the already existing index and dict file of genome in the config file, but it still showing that - 'not found in any config files provided to the pipeline' .

nf-core config memory variantcalling sarek
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updated by Maxime Garcia Maxime Garcia • written by ashaneev07 • ashaneev07

1 answer

I'd recommend adding any additional params for the pipeline in a params-file (https://www.nextflow.io/docs/latest/config.html#configuration-file https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files yaml and json format), and feed it on the command line with the -params-file option. That being said, given the error, I would also recommend to adjust the resource requirement for the pipeline and adapt to your own system/infrastructure cf https://nf-co.re/docs/usage/getting_started/configuration#max-resources.

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written by Maxime Garcia Maxime Garcia

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