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Commits (1)
#!/bin/bash -l
#SBATCH -p core
#SBATCH -n 1
#SBATCH -t 0:30:00
#SBATCH --mail-type=ALL
## stop on error but be verbose
set -e
......
#!/bin/bash -l
#SBATCH -p core -n 1
#SBATCH -t 0-01:00:00
#SBATCH --mail-type=ALL
usage() {
echo "usage: `basename $0` <fastq>
......
#!/bin/bash -l
#SBATCH -p core
#SBATCH -n 1
#SBATCH -t 8:00:00
#SBATCH --mail-type=ALL
## -A and --mail-user set in the submit job
## stop on error
set -ex
......
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......@@ -4,11 +4,6 @@
## but consider if we want that when reporting the Chimeric SAM (i.e. for merging the files, we would not want the reads to be part of the SAM...
## the good thing with outputting to SAM is that it can be readily piped into samtools -bs - | samtools sort - filename
#SBATCH -p core
#SBATCH -n 8
#SBATCH -t 0-02:00:00
#SBATCH --mail-type=ALL
#################
## Build geneModel
#################
......
#!/bin/bash -l
#SBATCH -p node
## for large files
## we don't need the proc but the mem
## we could give that as param
#SBATCH -n 16
## time too for large files
#SBATCH -t 12:00:00
#SBATCH --mail-type=ALL
## mail-user and A have to be set in the submit script
## stop on error
set -e
......
#!/bin/bash -l
#SBATCH -p node
#SBATCH -n 16
#SBATCH -t 3-00:00:00
#SBATCH --mail-type=ALL
## abort on error
set -e
......
#Example SLURM configuration for RNA seq pipeline
global_batch_args='--mail-type ALL'
fastqc_batch_args='--partition core --ntasks 1 -t 0:30:00'
fastqvalidator_batch_args='--partition core --ntasks 1 -t 1:00:00'
sortmerna_batch_args='--partition node --ntasks 16 -t 12:00:00'
trimmomatic_batch_args='--partition node --ntasks 16 -t 3-00:00:00'
star_batch_args='--partition core --ntasks 8 -t 2:00:00'
htseq_batch_args='--partition core --ntasks 1 -t 8:00:00'
# Example SLURM configuration for RNA seq pipeline
global_batch_args=' '
fastqc_batch_args='-q core -l procs=1 -l walltime=0:30:00'
fastqvalidator_batch_args='-q core -l procs=1 -l walltime=1:00:00'
sortmerna_batch_args='-q node -l procs=16 -l walltime=12:00:00'
trimmomatic_batch_args='-q node -l procs=16 -l walltime=3:00:00:00'
star_batch_args='-q core -l procs=8 -l walltime=2:00:00'
htseq_batch_args='-q core -l procs=1 -l walltime=8:00:00'