From 0a312cd2c91dfa397bcf23b67ac4867fca88e7dc Mon Sep 17 00:00:00 2001 From: "James A. Fellows Yates" Date: Thu, 7 May 2020 09:17:56 +0200 Subject: [PATCH] Update shh.md --- docs/pipeline/eager/shh.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/pipeline/eager/shh.md b/docs/pipeline/eager/shh.md index 6112842..41d0893 100644 --- a/docs/pipeline/eager/shh.md +++ b/docs/pipeline/eager/shh.md @@ -15,4 +15,4 @@ Example: `nextflow run nf-core/eager -profile shh` 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. -* Modifies the bwa aln `-n` parameter to 0.01, rather than typical default of 0.03, to syncronise the (unpublished) parameter with EAGER1 and typical/expected usage within the department. +* 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aln `-n` parameter to 0.01, rather than typical default of 0.04, and `-l` to 32 (rather than 1024) to syncronise the (unpublished) parameter with EAGER1 and typical/expected usage within the department.