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39 lines
1.6 KiB
Markdown
39 lines
1.6 KiB
Markdown
# nf-core/configs: CRA HPC Configuration
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nfcore pipeline sarek and rnaseq have been tested on the CRA HPC.
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## Before running the pipeline
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- You will need an account to use the CRA HPC cluster in order to run the pipeline.
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- Make sure that Singularity and Nextflow are installed.
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- Downlode pipeline singularity images to a HPC system using [nf-core tools](https://nf-co.re/tools/#downloading-pipelines-for-offline-use)
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```
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$ conda install nf-core
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$ nf-core download
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```
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- You will need to specify a Singularity cache directory in your ~./bashrc. This will store your container images in this cache directory without repeatedly downloading them every time you run a pipeline. Since space on home directory is limited, using lustre file system is recommended.
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```
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export NXF_SINGULARITY_CACHEDIR = "/lustre/fs0/storage/yourCRAAccount/cache_dir"
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```
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- Download iGenome reference to be used as a local copy.
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```
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$ aws s3 --no-sign-request --region eu-west-1 sync s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/ /lustre/fs0/storage/yourCRAAccount/references/Homo_sapiens/GATK/GRCh38/
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```
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## Running the pipeline using the adcra config profile
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- Run the pipeline within a [screen](https://linuxize.com/post/how-to-use-linux-screen/) or [tmux](https://linuxize.com/post/getting-started-with-tmux/) session.
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- Specify the config profile with `-profile adcra`.
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- Using lustre file systems to store results (`--outdir`) and intermediate files (`-work-dir`) is recommended.
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```
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nextflow run /path/to/nf-core/<pipeline-name> -profile adcra \
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--genome GRCh38 \
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--igenomes_base /path/to/genome_references/ \
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... # the rest of pipeline flags
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```
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