style: Run prettier
Edmund Miller
2 years ago
parent
58da86d729
commit
6c37bf3b20
@ -1,23 +1,23 @@
|
||||
# nf-core/configs: Crick (CAMP HPC) Configuration
|
||||
|
||||
All nf-core pipelines have 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.config) which has been pre-configured with a setup suitable for the CAMP HPC cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
|
||||
|
||||
Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on CAMP. Please check the main README of the pipeline to make sure that the version of Nextflow is compatible with that required to run the pipeline. You can do this by issuing the commands below:
|
||||
|
||||
```bash
|
||||
## Load Nextflow and Singularity environment modules
|
||||
module purge
|
||||
module load Nextflow/21.04.0
|
||||
module load Singularity/3.4.2
|
||||
```
|
||||
|
||||
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 is not 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://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.
|
||||
|
||||
>NB: You will need an account to use the HPC cluster on CAMP in order to run the pipeline. If in doubt contact IT.
|
||||
>NB: Nextflow will need to submit the jobs via SLURM to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.
|
||||
# nf-core/configs: Crick (CAMP HPC) Configuration
|
||||
|
||||
All nf-core pipelines have 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.config) which has been pre-configured with a setup suitable for the CAMP HPC cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
|
||||
|
||||
Before running the pipeline you will need to load Nextflow and Singularity using the environment module system on CAMP. Please check the main README of the pipeline to make sure that the version of Nextflow is compatible with that required to run the pipeline. You can do this by issuing the commands below:
|
||||
|
||||
```bash
|
||||
## Load Nextflow and Singularity environment modules
|
||||
module purge
|
||||
module load Nextflow/21.04.0
|
||||
module load Singularity/3.4.2
|
||||
```
|
||||
|
||||
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 is not 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://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.
|
||||
|
||||
> NB: You will need an account to use the HPC cluster on CAMP in order to run the pipeline. If in doubt contact IT.
|
||||
> NB: Nextflow will need to submit the jobs via SLURM to the HPC cluster and as such the commands above will have to be executed on one of the login nodes. If in doubt contact IT.
|
||||
|
||||
@ -1,22 +1,22 @@
|
||||
# nf-core/configs: Institute of Cancer Research (Davros HPC) Configuration
|
||||
|
||||
Deployment and testing of nf-core pipelines at the Davros cluster is on-going.
|
||||
|
||||
To run an nf-core pipeline on Davros, run the pipeline with `-profile icr_davros`. This will download and launch the [`icr_davros.config`](../conf/icr_davros.config) which has been pre-configured with a setup suitable for the Davros HPC cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
|
||||
|
||||
Before running the pipeline you will need to load Nextflow using the environment module system. You can do this by issuing the commands below:
|
||||
|
||||
```bash
|
||||
## Load Nextflow environment modules
|
||||
module load Nextflow/19.10.0
|
||||
```
|
||||
|
||||
Singularity is installed on the compute nodes of Davros, but not the login nodes. There is no module for Singularity.
|
||||
|
||||
A subset of the [AWS-iGenomes](https://github.com/ewels/AWS-iGenomes) resource has been made available locally on Davros so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline you want to execute. You can do this by simply using the `--genome <GENOME_ID>` parameter. Some of the more exotic genomes may not have been downloaded onto Davros so have a look in the `igenomes_base` path specified in [`icr_davros.config`](../conf/icr_davros.config), and if your genome of interest isn't present please contact [Scientific Computing](mailto:schelpdesk@icr.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://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. All of the main output files will be saved in the `results/` directory.
|
||||
|
||||
>NB: Nextflow will need to submit the jobs via LSF to the HPC cluster. This can be done from an interactive or normal job. If in doubt contact Scientific Computing.
|
||||
# nf-core/configs: Institute of Cancer Research (Davros HPC) Configuration
|
||||
|
||||
Deployment and testing of nf-core pipelines at the Davros cluster is on-going.
|
||||
|
||||
To run an nf-core pipeline on Davros, run the pipeline with `-profile icr_davros`. This will download and launch the [`icr_davros.config`](../conf/icr_davros.config) which has been pre-configured with a setup suitable for the Davros HPC cluster. Using this profile, a docker image containing all of the required software will be downloaded, and converted to a Singularity image before execution of the pipeline.
|
||||
|
||||
Before running the pipeline you will need to load Nextflow using the environment module system. You can do this by issuing the commands below:
|
||||
|
||||
```bash
|
||||
## Load Nextflow environment modules
|
||||
module load Nextflow/19.10.0
|
||||
```
|
||||
|
||||
Singularity is installed on the compute nodes of Davros, but not the login nodes. There is no module for Singularity.
|
||||
|
||||
A subset of the [AWS-iGenomes](https://github.com/ewels/AWS-iGenomes) resource has been made available locally on Davros so you should be able to run the pipeline against any reference available in the `igenomes.config` specific to the nf-core pipeline you want to execute. You can do this by simply using the `--genome <GENOME_ID>` parameter. Some of the more exotic genomes may not have been downloaded onto Davros so have a look in the `igenomes_base` path specified in [`icr_davros.config`](../conf/icr_davros.config), and if your genome of interest isn't present please contact [Scientific Computing](mailto:schelpdesk@icr.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://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. All of the main output files will be saved in the `results/` directory.
|
||||
|
||||
> NB: Nextflow will need to submit the jobs via LSF to the HPC cluster. This can be done from an interactive or normal job. If in doubt contact Scientific Computing.
|
||||
|
||||
Loading…
Reference in New Issue