From 28e59e38b4e73336109decbc3ea15b99deecb218 Mon Sep 17 00:00:00 2001 From: ameynert Date: Thu, 1 Sep 2022 09:28:05 +0100 Subject: [PATCH] Run prettier --- docs/adcra.md | 16 +++++++++++++--- 1 file changed, 13 insertions(+), 3 deletions(-) diff --git a/docs/adcra.md b/docs/adcra.md index 5e9d058..0494b5a 100644 --- a/docs/adcra.md +++ b/docs/adcra.md @@ -1,26 +1,36 @@ # nf-core/configs: CRA HPC Configuration + nfcore pipeline sarek and rnaseq have been tested on the CRA HPC. ## Before running the pipeline + - You will need an account to use the CRA HPC cluster in order to run the pipeline. - Make sure that Singularity and Nextflow are installed. - Downlode pipeline singularity images to a HPC system using [nf-core tools](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) + ``` $ conda install nf-core $ nf-core download ``` -- 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. + +- 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. + ``` export NXF_SINGULARITY_CACHEDIR = "/lustre/fs0/storage/yourCRAAccount/cache_dir" ``` + - Download iGenome reference to be used as a local copy. + ``` $ 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/ ``` + ## Running the pipeline using the adcra config profile + - 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. -- Specify the config profile with ```-profile adcra```. -- Using lustre file systems to store results (```--outdir```) and intermediate files (```-work-dir```) is recommended. +- Specify the config profile with `-profile adcra`. +- Using lustre file systems to store results (`--outdir`) and intermediate files (`-work-dir`) is recommended. + ``` nextflow run /path/to/nf-core/ -profile adcra \ --genome GRCh38 \