millironx/nf-configs
1
0
Fork 0
mirror of https://github.com/MillironX/nf-configs.git synced 2024-11-10 20:13:09 +00:00
Code Issues Releases Packages Activity

Merge pull request #112 from drpatelh/master

Browse source 
Change iGenomes path after fullish sync
This commit is contained in:
Harshil Patel 2019-12-18 11:12:27 +00:00 committed by GitHub
commit 01b7357d1d
No known key found for this signature in database
GPG key ID: 4AEE18F83AFDEB23
2 changed files with 4 additions and 4 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

2
conf/crick.config
View file

@ -20,5 +20,5 @@ params {
max_cpus = 32
max_time = 72.h
igenomes_base = '/camp/svc/reference/Genomics/iGenomes'
igenomes_base = '/camp/svc/reference/Genomics/aws-igenomes'
}

6
docs/crick.md
View file

@ -9,13 +9,13 @@ Before running the pipeline you will need to load Nextflow and Singularity using
```bash
## Load Nextflow and Singularity environment modules
module purge
module load Nextflow/0.32.0
module load Nextflow/19.10.0
module load Singularity/2.6.0-foss-2016b
```
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. You 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).
A local copy of the [AWS-iGenomes](https://github.com/ewels/AWS-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. You 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).
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://nf-co.re/usage/reference_genomes) for instructions).
All of the intermediate files required to run the pipeline will be stored in the `work/` directory. It is recommended to delete this directory after the pipeline has finished successfully because it can get quite large, and all of the main output files will be saved in the `results/` directory anyway.