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Fix HiTE arguments for v3.3.3 and adjusted hite resources on Myriad … #12

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Fix HiTE arguments for v3.3.3 and adjusted hite resources on Myriad … #12

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9 changes: 5 additions & 4 deletions modules/local/hite.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ process HITE {
label 'process_single'
label 'process_long'
tag "$species"
container = 'kanghu/hite:3.2.0'
container = 'kanghu/hite:3.3.3'
stageInMode = 'copy'

input:
Expand Down Expand Up @@ -34,14 +34,15 @@ process HITE {
cd /HiTE


python main.py --genome \${newpath} --outdir \${mydir}/${species}_hite_results --thread ${task.cpus}
python main.py --work_dir \${mydir} --genome \${newpath} --out_dir \${mydir}/${species}_hite_results --thread ${task.cpus} --annotate 1 --plant 0

cd \${mydir}/${species}_hite_results/

cat <<-END_VERSIONS > versions.yml
cat <<-END_VERSIONS > \${mydir}/versions.yml

"${task.process}":
Python version: \$(python --version | cut -f 2 -d " ")
HiTE version: 3.2.0
HiTE version: 3.3.3
Repeat Masker version: \$(RepeatMasker | grep version | cut -f 3 -d " ")
Repeat Modeler version: \$(RepeatModeler | grep /opt/conda/envs/HiTE/share/RepeatModeler/RepeatModeler | cut -f 3 -d " ")
LTRPipeline version: \$(LTRPipeline -version)
Expand Down
37 changes: 37 additions & 0 deletions ucl_myriad.config
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@@ -0,0 +1,37 @@
params {
config_profile_description = 'University College London Myriad cluster'
config_profile_contact = 'Chris Wyatt (ucbtcdr@ucl.ac.uk), Fernando Duarte (f.frutos@ucl.ac.uk)'
config_profile_url = 'https://www.rc.ucl.ac.uk/docs/Clusters/Myriad/'
}

executor {
name = 'sge'
queueSize = 100 // Limit number of jobs sent to qsub (max is 1000, but in case user submits more than one job)
submitRateLimit = '10/1s' // Submit max 10 jobs per second. To ease pressure on scheduler.
}

process {
penv = 'smp'
clusterOptions = {
def mem = task.memory.mega
def cpus = task.cpus
def memoryPerCpu = mem / task.cpus // We need memory per cpu, as is not possible to request memory per job
def baseOpts = "-S /bin/bash -l mem=${memoryPerCpu}M "
return baseOpts
}
scratch = false
}

singularity {
enabled = true
autoMounts = true
cacheDir = "${System.getenv('HOME')}/Scratch/.apptainer/pull"
runOptions = "-B ${System.getenv('HOME')},${System.getenv('PWD')} --no-mount /scratch --writable-tmpfs"
}

process {
withName: HITE {
memory = '64.GB'
cpus = 12
}
}