iGenomes
This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
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This page is a set of instructions to utilize the Genome parameter of the rnaseq nf-core pipeline. It requires you to download the necessary resources.
Was this helpful?
iGenomes are a collection of sequence and annotation files for commonly analyzed genomes. Each iGenome contains data for one species, downloaded from one source (UCSC, NCBI, or Ensembl), for one genomic build. They are available and easy to use, but not recommended because gene annotations are out of date and some iGenomes references (e.g., GRCh38) point to annotation files that use gene symbols as the primary identifier.
nf-core requires a configuration file to use iGenomes resources. That file is pipeline/conf/igenomes.config.
When you set the Genome parameter to any of the choices in the igenomes.config, the variables described in the json will be assumed. It is critical your S3 directory structure match this file and path structure because your igenomes.base will be the prefix of your S3 bucket the contents reside within. That is the text in {curly brackets}.
This command can be run from a Capsule by Reproducible Run or Cloud Workstation. It will download the necessary resources required for the GRCh37 into your Results folder.
You can use this to create a query to download the required files. For instance,
Next create an from the Results.
To use External Data Assets in a Pipeline, must be configured. If this isn't configured in your deployment or you're unsure if it is, contact your Code Ocean admin.
The path structure must be identical to the (picture above) for parameter - GRCh37.
If your directory structure is as shown in the file, iGenomes resources for your chosen genome will be downloaded into your bucket.
