From 88debfb87a7e01a62b109b74c6d04f63b3ebe27e Mon Sep 17 00:00:00 2001
From: Valentina Galata <valentina.galata@uni.lu>
Date: Sun, 16 Aug 2020 19:38:14 +0200
Subject: [PATCH] GDB config: sormerna update
---
config/GDB/config.yaml | 10 ++++++----
config/GDB/slurm.yaml | 2 +-
2 files changed, 7 insertions(+), 5 deletions(-)
diff --git a/config/GDB/config.yaml b/config/GDB/config.yaml
index 5fdb605..1c1d55e 100644
--- a/config/GDB/config.yaml
+++ b/config/GDB/config.yaml
@@ -74,13 +74,15 @@ fastp:
# rRNA gene filtering
sortmerna:
- threads: 20
+ threads: 28
# References to be used (w/ md5sums)
refs: [
- # db6e72022cf650c4b33bd888b92a0391 silva-bac-16s-id90.fasta
+ "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-arc-16s-id95.fasta",
+ "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-arc-23s-id98.fasta",
"/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-bac-16s-id90.fasta",
- # f347d2f8f8ffbfa28c785e3a9fe3db79 silva-bac-23s-id98.fasta
- "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-bac-23s-id98.fasta"
+ "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-bac-23s-id98.fasta",
+ "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-euk-18s-id95.fasta",
+ "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-euk-28s-id98.fasta"
]
# FastQ QC
diff --git a/config/GDB/slurm.yaml b/config/GDB/slurm.yaml
index 2e16e20..c39f241 100644
--- a/config/GDB/slurm.yaml
+++ b/config/GDB/slurm.yaml
@@ -240,7 +240,7 @@ tax_kraken2_lr:
n: 1
explicit: ""
-tax_kaiju_cdhit:
+tax_kaiju:
time: "00-00:30:00"
partition: "bigmem"
qos: "qos-bigmem"
--
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