To use this custom configuration, run the pipeline with -profile sage. This will download and load the sage.config, which contains a number of optimizations relevant to Sage employees running workflows on AWS (e.g. using Nextflow Tower). This profile will also load any applicable pipeline-specific configuration.
This global configuration includes the following tweaks:
- Update the default value for
igenomes_basetos3://sage-igenomes - Enable retries for all failures
- Allow pending jobs to finish if the number of retries are exhausted
- Increase resource allocations for specific resource-related exit codes
- Optimize resource allocations to better "fit" EC2 instance types
- Slow the increase in the number of allocated CPU cores on retries
- Increase the default time limits because we run pipelines on AWS
- Increase the amount of time allowed for file transfers
- Improve reliability of file transfers with retries and reduced concurrency
The following iGenomes prefixes have been copied from s3://ngi-igenomes/ (eu-west-1) to s3://sage-igenomes (us-east-1). See this script for more information. The sage-igenomes S3 bucket has been configured to openly available, but files cannot be downloaded out of us-east-1 to avoid egress charges. You can check the conf/igenomes.config file in each nf-core pipeline to figure out the mapping between genome IDs (i.e. for --genome) and iGenomes prefixes (example).
- Human Genome Builds
Homo_sapiens/Ensembl/GRCh37Homo_sapiens/GATK/GRCh37Homo_sapiens/UCSC/hg19Homo_sapiens/GATK/GRCh38Homo_sapiens/NCBI/GRCh38Homo_sapiens/UCSC/hg38
- Mouse Genome Builds
Mus_musculus/Ensembl/GRCm38Mus_musculus/UCSC/mm10