Commit 7bca601e authored by Valentina Galata's avatar Valentina Galata
Browse files

GDB config: sormerna cores and runtime, other minor changes

parent 3a42ed49
......@@ -74,7 +74,7 @@ fastp:
# rRNA gene filtering
sortmerna:
threads: 30
threads: 20
# References to be used (w/ md5sums)
refs: [
# db6e72022cf650c4b33bd888b92a0391 silva-bac-16s-id90.fasta
......@@ -95,7 +95,7 @@ fastqc:
# List of assemblers for different read types: assembler names MUST be UNIQUE
assemblers:
sr: ["megahit", "metaspades"]
lr: ["flye", "wtdbg2"]
lr: ["flye", "wtdbg2", "canu"]
hy: ["metaspadeshybrid", "operams"]
hyhy: []
......
......@@ -11,8 +11,6 @@
# conda env name or path
ONTP_ENV="ONT_pilot"
# number of concurrent jobs
ONTP_JOBS=10
# config files
ONTP_CONFIG="config/GDB/config.yaml"
ONTP_SLURM="config/GDB/slurm.yaml"
......@@ -21,6 +19,6 @@ ONTP_CLUSTER="sbatch -p {cluster.partition} -q {cluster.qos} {cluster.explicit}
conda activate ${ONTP_ENV}
snakemake -s workflow/Snakefile -rp --jobs ${ONTP_JOBS} --local-cores 1 \
snakemake -s workflow/Snakefile -rp --jobs 10 --local-cores 1 \
--configfile ${ONTP_CONFIG} --use-conda --conda-prefix ${CONDA_PREFIX}/pipeline \
--cluster-config ${ONTP_SLURM} --cluster "${ONTP_CLUSTER}"
......@@ -28,7 +28,7 @@ fastp_sr:
explicit: ""
sortmerna_filt:
time: "01-00:00:00"
time: "01-12:00:00"
partition: "batch"
qos: "qos-batch"
nodes: 1
......
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