From 3df1c26a8b54eb83880a0944b9bca5991f697d6f Mon Sep 17 00:00:00 2001
From: Valentina Galata <valentina.galata@uni.lu>
Date: Mon, 17 Aug 2020 14:45:00 +0200
Subject: [PATCH] GIS20/Zymo config: sortmerna/bbmap update
---
config/GIS20/config.yaml | 28 +++++++++++++++++++++-------
config/GIS20/slurm.yaml | 4 ++--
config/Zymo/config.yaml | 28 +++++++++++++++++++++-------
config/Zymo/slurm.yaml | 4 ++--
4 files changed, 46 insertions(+), 18 deletions(-)
diff --git a/config/GIS20/config.yaml b/config/GIS20/config.yaml
index ff1f487..66558bf 100644
--- a/config/GIS20/config.yaml
+++ b/config/GIS20/config.yaml
@@ -72,12 +72,6 @@ fastp:
threads: 10
min_length: 40
-# rRNA gene filtering
-sortmerna:
- threads: 20
- # References to be used (w/ md5sums)
- refs: []
-
# FastQ QC
# https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
fastqc:
@@ -197,9 +191,29 @@ barrnap:
cdhit:
threads: 10
-# XXX
+# https://sourceforge.net/projects/bbmap/
+# https://github.com/BioInfoTools/BBMap/
bbmap:
threads: 10
+ # References to be used (w/ md5sums)
+ rrna_refs: [
+ # c0cd2aa2e84e3e3977859c34feb63cd5 /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/rfam-5.8s-database-id98.fasta
+ # 703e4c270ab0a578deb4800c33b36367 /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/rfam-5s-database-id98.fasta
+ # 8b4e6c6f17f6f35444a60fdc915e052c /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-arc-16s-id95.fasta
+ # ca4edcdddb98d7868f93e2308e297704 /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-arc-23s-id98.fasta
+ # db6e72022cf650c4b33bd888b92a0391 /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-bac-16s-id90.fasta
+ # f347d2f8f8ffbfa28c785e3a9fe3db79 /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-bac-23s-id98.fasta
+ # 878a413765d09c3ec75409fb1d1573f1 /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-euk-18s-id95.fasta
+ # cbb973e63f52981bd591de0404df5839 /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-euk-28s-id98.fast
+ "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/rfam-5.8s-database-id98.fasta",
+ "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/rfam-5s-database-id98.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",
+ "/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"
+ ]
# Assembly quality
# https://github.com/ablab/quast
diff --git a/config/GIS20/slurm.yaml b/config/GIS20/slurm.yaml
index b5ad319..34e7b61 100644
--- a/config/GIS20/slurm.yaml
+++ b/config/GIS20/slurm.yaml
@@ -27,8 +27,8 @@ fastp_sr:
n: 1
explicit: ""
-sortmerna_filt:
- time: "00-12:00:00"
+rm_rrna_bbmap:
+ time: "00-6:00:00"
partition: "batch"
qos: "qos-batch"
nodes: 1
diff --git a/config/Zymo/config.yaml b/config/Zymo/config.yaml
index 0d6869f..a496f39 100755
--- a/config/Zymo/config.yaml
+++ b/config/Zymo/config.yaml
@@ -72,12 +72,6 @@ fastp:
threads: 10
min_length: 40
-# rRNA gene filtering
-sortmerna:
- threads: 20
- # References to be used (w/ md5sums)
- refs: []
-
# FastQ QC
# https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
fastqc:
@@ -197,9 +191,29 @@ barrnap:
cdhit:
threads: 10
-# XXX
+# https://sourceforge.net/projects/bbmap/
+# https://github.com/BioInfoTools/BBMap/
bbmap:
threads: 10
+ # References to be used (w/ md5sums)
+ rrna_refs: [
+ # c0cd2aa2e84e3e3977859c34feb63cd5 /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/rfam-5.8s-database-id98.fasta
+ # 703e4c270ab0a578deb4800c33b36367 /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/rfam-5s-database-id98.fasta
+ # 8b4e6c6f17f6f35444a60fdc915e052c /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-arc-16s-id95.fasta
+ # ca4edcdddb98d7868f93e2308e297704 /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-arc-23s-id98.fasta
+ # db6e72022cf650c4b33bd888b92a0391 /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-bac-16s-id90.fasta
+ # f347d2f8f8ffbfa28c785e3a9fe3db79 /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-bac-23s-id98.fasta
+ # 878a413765d09c3ec75409fb1d1573f1 /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-euk-18s-id95.fasta
+ # cbb973e63f52981bd591de0404df5839 /mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/silva-euk-28s-id98.fast
+ "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/rfam-5.8s-database-id98.fasta",
+ "/mnt/irisgpfs/projects/ecosystem_biology/local_tools/IMP3/databases/sortmerna/rfam-5s-database-id98.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",
+ "/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"
+ ]
# Assembly quality
# https://github.com/ablab/quast
diff --git a/config/Zymo/slurm.yaml b/config/Zymo/slurm.yaml
index d75fb43..6b8b90d 100644
--- a/config/Zymo/slurm.yaml
+++ b/config/Zymo/slurm.yaml
@@ -27,8 +27,8 @@ fastp_sr:
n: 1
explicit: ""
-sortmerna_filt:
- time: "01-12:00:00"
+rm_rrna_bbmap:
+ time: "00-6:00:00"
partition: "batch"
qos: "qos-batch"
nodes: 1
--
GitLab