mirror of
https://github.com/MillironX/nf-configs.git
synced 2024-11-10 20:13:09 +00:00
Properly changed link to crick.config
This commit is contained in:
parent
a2c848c8e4
commit
fd226aac33
1 changed files with 2 additions and 2 deletions
|
@ -2,7 +2,7 @@
|
|||
|
||||
This pipeline has been successfully configured for use on the CAMP HPC cluster at the [The Francis Crick Institute](https://www.crick.ac.uk/).
|
||||
|
||||
To use, run the pipeline with `-profile crick`. This will download and launch the [`crick.config`](../conf/crick.md) which has been pre-configured with a setup suitable for the CAMP HPC cluster. Using this profile, Nextflow will download a temporary singularity image with all of the required software before execution of the pipeline.
|
||||
To use, run the pipeline with `-profile crick`. This will download and launch the [`crick.config`](../conf/crick.config) which has been pre-configured with a setup suitable for the CAMP HPC cluster. Using this profile, Nextflow will download a temporary singularity image with all of the required software before execution of the pipeline.
|
||||
|
||||
Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on CAMP. You can do this by issuing the commands below:
|
||||
|
||||
|
@ -15,7 +15,7 @@ module load Singularity/2.6.0-foss-2016b
|
|||
nextflow run nf-core/atacseq -profile crick --genome GRCh37 --design /path/to/design.csv --email test.user@crick.ac.uk
|
||||
```
|
||||
|
||||
A local copy of the iGenomes resource has been made available on CAMP so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. Yuo can do this by simply using the `--genome <GENOME_ID>` parameter. Some of the more exotic genomes may not have been downloaded onto CAMP so have a look in the `igenomes_base` path specified in [`crick.config`](../conf/crick.md), and if your genome of interest isnt present please contact [BABS](mailto:bioinformatics@crick.ac.uk).
|
||||
A local copy of the iGenomes resource has been made available on CAMP so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline. Yuo can do this by simply using the `--genome <GENOME_ID>` parameter. Some of the more exotic genomes may not have been downloaded onto CAMP so have a look in the `igenomes_base` path specified in [`crick.config`](../conf/crick.config), and if your genome of interest isnt present please contact [BABS](mailto:bioinformatics@crick.ac.uk).
|
||||
|
||||
Alternatively, if you are running the pipeline regularly for genomes that arent available in the iGenomes resource, we recommend creating a config file with paths to your reference genome indices (see [`reference genomes documentation`](https://github.com/nf-core/atacseq/blob/master/docs/configuration/reference_genomes.md) for instructions).
|
||||
|
||||
|
|
Loading…
Reference in a new issue