Commit cb0e17b2 authored by Valentina Galata's avatar Valentina Galata
Browse files

updated GDB contig files

parent 4d60da61
......@@ -3,6 +3,8 @@
# Pipeline steps to be done: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
steps: ["preprocessing", "assembly", "mapping", "annotation", "analysis", "taxonomy"]
steps_annotation: ["diamond", "rgi", "plasflow", "minced"] # prodigal is run in any case
steps_analysis: ["quast", "cdhit", "mash_dist"]
############################################################
# INPUT
......@@ -77,11 +79,14 @@ fastqc:
##############################
# Assembly
# List of assemblers for different read types
# List of assemblers for different read types: assembler names MUST be UNIQUE
assemblers:
sr: ["megahit", "metaspades", "megahitmetatracon", "metaspadesmetatracon"]
# sr: ["megahit", "metaspades", "megahitmetatracon", "metaspadesmetatracon"]
# lr: ["flye"]
# hy: ["metaspadeshybrid", "operams", "metaspadeshybridmetatracon", "operamsmetatracon"]
sr: ["megahit", "metaspades"]
lr: ["flye"]
hy: ["metaspadeshybrid", "operams", "metaspadeshybridmetatracon", "operamsmetatracon"]
hy: ["metaspadeshybrid", "operams"]
# https://github.com/fenderglass/Flye
flye:
......
......@@ -5,14 +5,14 @@
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 1
#SBATCH --time=2-00:00:00
#SBATCH --time=1-00:00:00
#SBATCH -p batch
#SBATCH --qos=qos-batch
# conda env name or path
ONTP_ENV="ONT_pilot"
# number of concurrent jobs
ONTP_JOBS=10
ONTP_JOBS=20
# config files
ONTP_CONFIG="config/GDB/config.yaml"
ONTP_SLURM="config/GDB/slurm.yaml"
......
......@@ -152,7 +152,7 @@ polishing_metat_racon:
# Annotation
annotation_prodigal:
time: "01-4:00:00"
time: "00-2:00:00"
partition: "batch"
qos: "qos-batch"
nodes: 1
......
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