Commit 48aa5933 authored by Valentina Galata's avatar Valentina Galata
Browse files

updated GDB config files

parent 9fba72e5
......@@ -3,7 +3,7 @@
# Steps to be done
# steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
steps: ["assembly", "mapping", "annotation", "analysis", "taxonomy"]
steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
steps_annotation: ["diamond", "rgi", "plasflow", "minced", "barrnap"] # prodigal is run in any case
steps_analysis: ["quast", "cdhit", "mash_dist"]
steps_taxonomy: ["kraken2", "kaiju"]
......@@ -72,6 +72,17 @@ fastp:
threads: 10
min_length: 40
# rRNA gene filtering
sortmerna:
threads: 20
# References to be used (w/ md5sums)
refs: [
# db6e72022cf650c4b33bd888b92a0391 silva-bac-16s-id90.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"
]
# FastQ QC
# https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
fastqc:
......@@ -83,12 +94,10 @@ fastqc:
# List of assemblers for different read types: assembler names MUST be UNIQUE
assemblers:
# sr: ["megahit", "metaspades", "megahitmetatracon", "metaspadesmetatracon"]
# lr: ["flye"]
# hy: ["metaspadeshybrid", "operams", "metaspadeshybridmetatracon", "operamsmetatracon"]
sr: ["megahit", "metaspades"]
lr: ["flye", "wtdbg2", "canu"]
hy: ["metaspadeshybrid", "operams"]
hyhy: []
# https://github.com/fenderglass/Flye
flye:
......
......@@ -12,7 +12,7 @@
# conda env name or path
ONTP_ENV="ONT_pilot"
# number of concurrent jobs
ONTP_JOBS=5
ONTP_JOBS=10
# config files
ONTP_CONFIG="config/GDB/config.yaml"
ONTP_SLURM="config/GDB/slurm.yaml"
......
......@@ -27,6 +27,14 @@ fastp_sr:
n: 1
explicit: ""
sortmerna_filt:
time: "00-12:00:00"
partition: "batch"
qos: "qos-batch"
nodes: 1
n: 1
explicit: ""
# Assembly
assembly_lr_flye:
time: "00-8:00:00"
......@@ -143,7 +151,7 @@ polishing_lr_racon:
explicit: ""
polishing_lr_medaka:
time: "00-12:00:00"
time: "01-00:00:00"
partition: "bigmem"
qos: "qos-bigmem"
nodes: 1
......
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