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manifest {
name = "DEN-IM"
mainScript = "DEN-IM.nf"
version = "2.1"
}
params {
platformHTTP = null
reportHTTP = null
// Settings this option to true, will trigger the removal of temporary
// data (usually fastq reads) at particular checkpoint processes that
// modify that data. These checkpoint processes include 'trimmomatic',
// 'spades' and 'skesa'.
// WARNING: This will remove temporary fastq files that are not necessary
// for the completion of the pipeline but, consequently, will disable
// the resume functionality of the pipeline. However, it is often necessary
// for very large pipelines and whenever disk space is critical.
// More precisely, these checkpoint components will check whether the
// putative temporary files are inside the nextflow work directory by
// matching the regex: ".*/work/.{2}/.{30}/.*"
// If it is a match, then the file is assumed to be a temporary one and
// will be removed.
clearAtCheckpoint = false
}
env {
PYTHONPATH = "$baseDir/templates:\$PYTHONPATH"
PATH = "$baseDir/templates:\$PATH"
}
process {
cpus = 1
memory = "1GB"
errorStrategy = { task.attempt <= 7 ? "retry" : "ignore" }
maxRetries = 7
container = "flowcraft/flowcraft_base:1.0.0-1"
}
docker {
// Added default docker option to avoid docker permission errors. See issue
// #142
runOptions = "-u \$(id -u):\$(id -g)"
}
executor {
$local {
cpus = 4
}
}
singularity {
cacheDir = "$HOME/.singularity_cache"
autoMounts = true
}
trace {
enabled = true
file = "pipeline_stats.txt"
fields = "task_id,\
hash,\
process,\
tag,\
status,\
exit,\
start,\
container,\
cpus,\
time,\
disk,\
memory,\
duration,\
realtime,\
queue,\
%cpu,\
%mem,\
rss,\
vmem,\
rchar,\
wchar"
}
// PROFILE OPTIONS //
///////////////////////////////////////////////////////////////////////////////
profiles {
oneida {
process.executor = "slurm"
docker.enabled = true
process{
// MEMORY USAGE PER PROCESS //
// general memory usage
memory = "4GB"
}
}
// INCD PROFILE
incd {
process.executor = "slurm"
singularity.enabled = true
singularity {
cacheDir = "/mnt/singularity_cache"
autoMounts = true
}
// Error and retry strategies
process.errorStrategy = "retry"
maxRetries = 3
process.$chewbbaca.queue = "chewBBACA"
process {
// MEMORY USAGE PER PROCESS //
// general memory usage
memory = "4GB"
}
}
// SLURM PROFILE
slurm {
// Change executor for SLURM
process.executor = "slurm"
// Change container engine for Shifter
shifter.enabled = true
process {
clusterOptions = "--qos=oneida"
errorStrategy = "retry"
maxRetries = 5
// MEMORY USAGE PER PROCESS //
// general memory usage
memory = "4GB"
}
}
// SLURM PROFILE
slurmOneida {
// Change executor for SLURM
process.executor = "slurm"
// Change container engine for Shifter
shifter.enabled = true
process {
clusterOptions = "--qos=oneida"
// MEMORY USAGE PER PROCESS //
// general memory usage
memory = "4GB"
// Set QOS for chewbbaca in order to run a single job
$chewbbaca.clusterOptions = "--qos=chewbbaca"
}
}
}
includeConfig "profiles.config"
includeConfig "resources.config"
includeConfig "containers.config"
includeConfig "params.config"
includeConfig "user.config"
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