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22 lines
2.3 KiB
Markdown
22 lines
2.3 KiB
Markdown
# nf-core/configs: Institute of Cancer Research (Davros HPC) Configuration
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Deployment and testing of nf-core pipelines at the Davros cluster is on-going.
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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.
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Before running the pipeline you will need to load Nextflow using the environment module system. You can do this by issuing the commands below:
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```bash
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## Load Nextflow environment modules
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module load Nextflow/19.10.0
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```
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Singularity is installed on the compute nodes of Davros, but not the login nodes. There is no module for Singularity.
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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).
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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).
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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.
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> 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.
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