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50 lines
2.3 KiB
Markdown
50 lines
2.3 KiB
Markdown
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# nf-core/atacseq: Reference Genomes Configuration
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The nf-core/atacseq pipeline needs a reference genome for alignment and annotation.
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These paths can be supplied on the command line at run time (see the [usage docs](../usage.md)),
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but for convenience it's often better to save these paths in a nextflow config file.
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See below for instructions on how to do this.
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Read [Adding your own system](adding_your_own.md) to find out how to set up custom config files.
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## Adding paths to a config file
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Specifying long paths every time you run the pipeline is a pain.
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To make this easier, the pipeline comes configured to understand reference genome keywords which correspond to preconfigured paths, meaning that you can just specify `--genome ID` when running the pipeline.
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Note that this genome key can also be specified in a config file if you always use the same genome.
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To use this system, add paths to your config file using the following template:
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```nextflow
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params {
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genomes {
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'YOUR-ID' {
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fasta = '<PATH TO FASTA FILE>/genome.fa'
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}
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'OTHER-GENOME' {
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// [..]
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}
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}
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// Optional - default genome. Ignored if --genome 'OTHER-GENOME' specified on command line
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genome = 'YOUR-ID'
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}
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```
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You can add as many genomes as you like as long as they have unique IDs.
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## illumina iGenomes
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To make the use of reference genomes easier, illumina has developed a centralised resource called [iGenomes](https://support.illumina.com/sequencing/sequencing_software/igenome.html).
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Multiple reference index types are held together with consistent structure for multiple genomes.
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We have put a copy of iGenomes up onto AWS S3 hosting and this pipeline is configured to use this by default.
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The hosting fees for AWS iGenomes are currently kindly funded by a grant from Amazon.
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The pipeline will automatically download the required reference files when you run the pipeline.
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For more information about the AWS iGenomes, see https://ewels.github.io/AWS-iGenomes/
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Downloading the files takes time and bandwidth, so we recommend making a local copy of the iGenomes resource.
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Once downloaded, you can customise the variable `params.igenomes_base` in your custom configuration file to point to the reference location.
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For example:
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```nextflow
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params.igenomes_base = '/path/to/data/igenomes/'
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```
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