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

Question

[ashaneev07]

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' .

Answer 1

[Maxime Garcia]

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.