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nextflow.config
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manifest {
author = "Sophie-Luise Heidig"
version = "1.0.0"
homePage =
mainScript = "achro.nf"
name = "achro"
description = "stuff"
defaultBranch = "main"
}
//create unique output folders
params.executionTimestamp = new java.text.SimpleDateFormat("yyyy_MM_dd_HH_mm_ss").format(new Date())
//Parameters to adapt run to dataset
params.condaEnvPath = false
params.data = "$launchDir/data"
params.outFolder = "$launchDir/"
params.structures = false
params.predictRemaining = false
params.orthoGroupSeqs = false
params.minCoverage = 0.8
params.outGroup = false
params.foldseekClusters = false
report {
enabled = false
file = "$params.outFolder/nextflow_report.html"
overwrite = true
}
trace {
enabled = false
raw = true
file = "$params.outFolder/resources.txt"
overwrite = true
}
profiles {
standard {
process {
executor = 'local'
conda = "${params.condaEnvPath ? params.condaEnvPath : 'recipes/conda_env_m_apple_simsapiper.yml'}"
container = 'slheidig/simsapiper:05'
}
}
hydra {
singularity {
enabled = true
cacheDir = "$VSC_SCRATCH_VO_USER/.apptainer"
}
process {
executor = 'local'
cpus ='1'
//memory ='4 GB'
//time ='10min'
pollInterval = '5 sec'
queueSize = 50
//module = 'Biopython/1.79-foss-2022a:SciPy-bundle/2022.05-foss-2022a:matplotlib/3.5.2-foss-2022a'
withName:'runOrthofinder'{
executor = 'slurm'
cpus = '20'
memory = 40.GB
time = '2.h '
container="/scratch/brussel/vo/000/bvo00023/vsc10579/.apptainer/orthofinder.sif"
}
//withName:'runCDHIT'{
// module = 'CD-HIT/4.8.1-GCC-11.3.0:BLAST+/2.13.0-gompi-2022a'
//}
withName:'predictStructures'{
executor = 'slurm'
module = 'legacy-software:ESM-2/2.0.0-foss-2021a-CUDA-11.3.1:OpenFold/1.0.1-foss-2021a-CUDA-11.3.1'
time = { 15.h * task.attempt }
memory = { 20.GB }
clusterOptions = "--partition=ampere_gpu --nodes=1 --gpus-per-node=1 --ntasks-per-gpu=1 --cpus-per-gpu=8"
}
withName:'runFoldseek'{
executor = 'slurm'
cpus = '10'
memory = 20.GB
time = '30min'
//container="/scratch/brussel/vo/000/bvo00023/vsc10579/.apptainer/foldseek.sif"
//clusterOptions = "--begin=now+60"
}
}
}
withdocker {
docker.enabled = true
singularity.enabled = false
docker.temp = 'auto'
}
withsingularity {
docker.enabled = false
singularity {
enabled = true
runOptions = "-B /run"
}
}
withconda {
conda.enabled = true
}
}