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Mention SHH EAGER group-specific profiles

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James A. Fellows Yates 2020-05-26 11:14:42 +02:00 committed by GitHub
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docs/pipeline/eager/shh.md
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@ -14,5 +14,5 @@ Example: `nextflow run nf-core/eager -profile shh`
Specific configurations for shh has been made for eager. Specific configurations for shh has been made for eager.
* If running with the MALT module turned on, the MALT process by default will be sent to the long queue with a resource requirement minimum of 725GB and 64 cores. If this fails, the process will be tried once more only and sent to the supercruncher queue. The module will not retry after this, and pipeline will fail. * If running with the MALT module turned on, the MALT process by default will be sent to the long queue with a resource requirement minimum of 725GB and 64 cores. If this fails, the process will be tried once more only and sent to the supercruncher queue. The module will not retry after this, and pipeline will fail. Note, this will only work on SDAG.
* Modifies the bwa aln `-n` parameter to 0.01, rather than typical default of 0.04, and `-l` to 32 (rather than 1024) to syncronise the (unpublished) parameter with EAGER1 and typical/expected usage within the department. * Provides additional group specific profiles, which adapt the `bwa aln` mapping parameters to each context: `pathogens_loose` (`-l 0.01 -n 16`), `pathogens_strict` (`-l 32, -n 0.1`) and `human` (`-l 16500, -n 0.01`).