Specify additional flags when submitting cluster PECAT job

[dmacguigan]

Hello,

Is there a way to specify additional flags/options when submitting a PECAT job on a computing cluster? For example, I would need to include some required information specific to my university's cluster, such as:

#SBATCH --reservation=ubhpc-future
#SBATCH --qos=general-compute
#SBATCH --partition=general-compute

I assume I could edit the individual scirpts (like prp_job.sh), but it would be much easier if I could specify these options in the config file.

Here is my config file:

project=Emac_PECAT
reads=/vscratch/grp-tkrabben/MacGuigan/rawNanoporeData/Emac/Emac.cell1.passed.fastq
genome_size=800000000
threads=14
cleanup=1
grid=slurm:8
prep_min_length=7000
prep_output_coverage=60
corr_iterate_number=1
corr_block_size=1000000000
corr_correct_options=--score=weight:lc=16 --aligner edlib --filter1 oh=1000:ohr=0.01 --candid>
corr_filter_options=--filter0=l=7000:al=3500:alr=0.5:aal=10000:oh=5000:ohr=0.3
corr_rd2rd_options=-x ava-ont
corr_output_coverage=60
phase_method = 0
polish_medaka = 0
#align_block_size=4000000000
#align_rd2rd_options=-X -g3000 -w30 -k19 -m100 -r500
#align_filter_options=--filter0=l=5000:aal=6000:aalr=0.5:oh=3000:ohr=0.3 --task=extend --filter1=oh=300:ohr=0.03
#asm1_assemble_options=
#phase_method=0
#phase_rd2ctg_options=-x map-ont -c -p 0.5 -r 1000
#phase_use_reads=1
#phase_phase_options= --coverage lc=30 --phase_options icr=0.2:icc=6:sc=8
#phase_filter_options= --threshold=1000
#asm2_assemble_options=
#polish_use_reads=0
#polish_filter_options= --filter0 oh=1000:ohr=0.1
#polish_map_options = -x map-ont -k19 -w10
#polish_cns_options =

Thanks, Dan

[lemene]

hi, @dmacguigan

The parameter grid_options may be helpful. Here is my example.

When grid_options is set to

grid_options=  -A pi_zy --partition cpuQ -q cpuq

, the submit command is

sbatch -D `pwd` -J al_rd2rd_split.sh --cpus-per-task=1 -o al_rd2rd_split.sh.log -A pi_zy --partition cpuQ -q cpuq al_rd2rd_split.sh

[dmacguigan]

Hi @lemene,

Thanks, that did the trick! Might I suggest adding grid_options= to the config file README?

[lemene]

Thank you for your suggestion. I have added it to README.md and config.md