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30 lines
2 KiB
Markdown
30 lines
2 KiB
Markdown
# nf-core/configs: Sage Bionetworks Global Configuration
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To use this custom configuration, run the pipeline with `-profile sage`. This will download and load the [`sage.config`](../conf/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.
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This global configuration includes the following tweaks:
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- Update the default value for `igenomes_base` to `s3://sage-igenomes`
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- Enable retries by default when exit codes relate to insufficient memory
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- Allow pending jobs to finish if the number of retries are exhausted
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- Increase the amount of time allowed for file transfers
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- Increase the default chunk size for multipart uploads to S3
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- Slow down job submission rate to avoid overwhelming any APIs
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- Define the `check_max()` function, which is missing in Sarek v2
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- Slow the increase in the number of allocated CPU cores on retries
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- Increase the default time limits because we run pipelines on AWS
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## Additional information about iGenomes
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The following iGenomes prefixes have been copied from `s3://ngi-igenomes/` (`eu-west-1`) to `s3://sage-igenomes` (`us-east-1`). See [this script](https://github.com/Sage-Bionetworks-Workflows/nextflow-infra/blob/main/bin/mirror-igenomes.sh) 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](https://github.com/nf-core/rnaseq/blob/89bf536ce4faa98b4d50a8ec0a0343780bc62e0a/conf/igenomes.config#L14-L26)).
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- **Human Genome Builds**
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- `Homo_sapiens/Ensembl/GRCh37`
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- `Homo_sapiens/GATK/GRCh37`
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- `Homo_sapiens/UCSC/hg19`
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- `Homo_sapiens/GATK/GRCh38`
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- `Homo_sapiens/NCBI/GRCh38`
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- `Homo_sapiens/UCSC/hg38`
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- **Mouse Genome Builds**
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- `Mus_musculus/Ensembl/GRCm38`
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- `Mus_musculus/UCSC/mm10`
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