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- removed mention of iGenomes
- clarified whom to contact for support
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Gwenna Breton 2022-07-06 11:20:59 +02:00 committed by GitHub
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docs/medair.md
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@ -57,12 +57,5 @@ Depending on what you are running, you can choose between the `wgs` and `product
>Usage: -profile medair,wgs ?? (Check) >Usage: -profile medair,wgs ?? (Check)
## iGenomes specific configuration >NB: You will need an account to use the HPC cluster on PROFILE CLUSTER in order to run the pipeline. If in doubt contact cgg-it.
>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact cgg-it.
>TODO modify this part. Do we want to have the iGenomes somewhere?
A local copy of the iGenomes resource has been made available on PROFILE CLUSTER so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline.
You can do this by simply using the `--genome <GENOME_ID>` parameter.
>NB: You will need an account to use the HPC cluster on PROFILE CLUSTER in order to run the pipeline. If in doubt contact IT.
>NB: Nextflow will need to submit the jobs via the job scheduler to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.