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nf-core/configs: Seadragon Configuration

To use, run a pipeline with -profile seadragon. This will download and launch the seadragon.config, which has been pre-configured with a setup suitable for the Seadragon HPC environment at The University of Texas MD Anderson Cancer Center. Using this profile, container images with all required software will be pulled and converted to Singularity images before job execution.

Module Requirements

In order to run a pipeline on the Seadragon environment, you will need to load the following modules:

module load Nextflow

iGenomes Resource

A local copy of the iGenomes resource is available on Seadragon /rsrch3/scratch/reflib/REFLIB_data/AWS-iGenomes/ . You can reference it by using the --genome <GENOME_ID> parameter in an igenomes-supporting nf-core pipeline. This ensures that all genome-specific references are correctly configured and optimized for the cluster.

Notes

  • Data Storage: All intermediate files will be stored in the work/ directory within the job's launch directory. On a successful completion of a run, these will be automatically deleted as these files can consume significant space. If a pipeline run fails, it will not be deleted. You can preserve all intermediate files by using -profile debug,seadragon.
  • User Access: Ensure that you have an active account to use Seadragon. If unsure, contact the HPC support team at The University of Texas MD Anderson Cancer Center.
  • Job Submission: Nextflow jobs must be submitted from the login nodes of Seadragon. If in doubt, refer to the cluster documentation or contact support.

Example Command

nextflow run nf-core/rnaseq --reads '*_R{1,2}.fastq.gz' --genome GRCh38 -profile seadragon

Further Information

For more details about seadragon cluster, visit the Seadragon HPC webpage: https://hpcweb.mdanderson.edu/