mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-25 17:29:55 +00:00
Bit of restructuring
This commit is contained in:
parent
0c598846e0
commit
64dd812fad
2 changed files with 0 additions and 49 deletions
|
@ -1,49 +0,0 @@
|
||||||
# nf-core/atacseq: Reference Genomes Configuration
|
|
||||||
|
|
||||||
The nf-core/atacseq pipeline needs a reference genome for alignment and annotation.
|
|
||||||
|
|
||||||
These paths can be supplied on the command line at run time (see the [usage docs](../usage.md)),
|
|
||||||
but for convenience it's often better to save these paths in a nextflow config file.
|
|
||||||
See below for instructions on how to do this.
|
|
||||||
Read [Adding your own system](adding_your_own.md) to find out how to set up custom config files.
|
|
||||||
|
|
||||||
## Adding paths to a config file
|
|
||||||
Specifying long paths every time you run the pipeline is a pain.
|
|
||||||
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.
|
|
||||||
|
|
||||||
Note that this genome key can also be specified in a config file if you always use the same genome.
|
|
||||||
|
|
||||||
To use this system, add paths to your config file using the following template:
|
|
||||||
|
|
||||||
```nextflow
|
|
||||||
params {
|
|
||||||
genomes {
|
|
||||||
'YOUR-ID' {
|
|
||||||
fasta = '<PATH TO FASTA FILE>/genome.fa'
|
|
||||||
}
|
|
||||||
'OTHER-GENOME' {
|
|
||||||
// [..]
|
|
||||||
}
|
|
||||||
}
|
|
||||||
// Optional - default genome. Ignored if --genome 'OTHER-GENOME' specified on command line
|
|
||||||
genome = 'YOUR-ID'
|
|
||||||
}
|
|
||||||
```
|
|
||||||
|
|
||||||
You can add as many genomes as you like as long as they have unique IDs.
|
|
||||||
|
|
||||||
## illumina iGenomes
|
|
||||||
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).
|
|
||||||
Multiple reference index types are held together with consistent structure for multiple genomes.
|
|
||||||
|
|
||||||
We have put a copy of iGenomes up onto AWS S3 hosting and this pipeline is configured to use this by default.
|
|
||||||
The hosting fees for AWS iGenomes are currently kindly funded by a grant from Amazon.
|
|
||||||
The pipeline will automatically download the required reference files when you run the pipeline.
|
|
||||||
For more information about the AWS iGenomes, see https://ewels.github.io/AWS-iGenomes/
|
|
||||||
|
|
||||||
Downloading the files takes time and bandwidth, so we recommend making a local copy of the iGenomes resource.
|
|
||||||
Once downloaded, you can customise the variable `params.igenomes_base` in your custom configuration file to point to the reference location.
|
|
||||||
For example:
|
|
||||||
```nextflow
|
|
||||||
params.igenomes_base = '/path/to/data/igenomes/'
|
|
||||||
```
|
|
Loading…
Reference in a new issue