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nextflow.config
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nextflow.config
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//============================================================================//
// Define params
//============================================================================//
// Global input
//============================================================================//
params.in_files = "input/*fasta"
params.out_dir = 'output'
params.entry_point = "mmseqs" // options: 'mmseqs' or 'colabfold'
// colabfold workflow inputs
//============================================================================//
// mmseqs
params.reference_fasta = ""
// colabfold
params.COLABFOLD_num_recycles = 3
params.COLABFOLD_stop_at_score = 70
params.COLABFOLD_stop_at_score_below = 40
params.COLABFOLD_num_models = 3
//============================================================================//
// Other settings
//============================================================================//
trace.overwrite = true
//============================================================================//
// Process
//============================================================================//
profiles {
sge {
process {
// Global setting
executor = 'sge'
penv = 'smp'
clusterOptions = { '-V -S /bin/bash' }
cache = 'lenient'
//conda = "$baseDir/resources/conda/conda_linux.yml"
// Error handling
errorStrategy = 'retry'
maxRetries = 2
// resources
withName: mmseqs2 {
beforeScript = "module load Sali gcc/10.2.1 || true"
time = { 1.h * task.attempt }
memory = { 30.GB * task.attempt }
cpus = { 5 * task.attempt }
// queue = { task.time < 30.m ? "short.q" : "long.q" } - not needed in wynton
}
withName: colabfold {
beforeScript = "module load Sali gcc/10.2.1 cuda/11.5.0 || true ; export CUDA_VISIBLE_DEVICES=\$SGE_GPU"
time = { 119.m * task.attempt }
memory = { 20.GB + 10.GB * task.attempt }
cpus = 1
queue = "gpu.q"
}
}
//============================================================================//
// Misc settings
//============================================================================//
executor {
// Let nextflow submit up to this many jobs in parallel at one time
queueSize = 150
}
report {
enabled = true
file = "$params.out_dir/nf_information/pipeline_report.html"
}
timeline {
enabled = true
file = "$params.out_dir/nf_information/timeline.html"
}
trace {
enabled = true
file = "$params.out_dir/nf_information/trace.tsv"
}
conda {
cacheDir = "/wynton/group/gladstone/users/jnomburg/software/nf_conda_envs"
}
} // this closes the sge profile
mac {
process {
// Global setting
// Error handling
errorStrategy = 'retry'
maxRetries = 2
// resources
withName: mmseqs2 {
time = 1.h
memory = 10.GB
cpus = 5
}
}
//============================================================================//
// Misc settings
//============================================================================//
report {
enabled = true
file = "$params.out_dir/nf_information/pipeline_report.html"
}
timeline {
enabled = true
file = "$params.out_dir/nf_information/timeline.html"
}
trace {
enabled = true
file = "$params.out_dir/nf_information/trace.tsv"
}
} // this closes the mac profile
docker {
process {
// Global setting
docker.enabled = true
// Error handling
errorStrategy = 'retry'
maxRetries = 2
// resources
withName: mmseqs2 {
container = "quay.io/biocontainers/mmseqs2"
time = 1.h
memory = 10.GB
cpus = 5
}
}
//============================================================================//
// Misc settings
//============================================================================//
report {
enabled = true
file = "$params.out_dir/nf_information/pipeline_report.html"
}
timeline {
enabled = true
file = "$params.out_dir/nf_information/timeline.html"
}
trace {
enabled = true
file = "$params.out_dir/nf_information/trace.tsv"
}
} // this closes the docker profile
hybrid {
process {
withName: mmseqs2 {
beforeScript = "module load Sali gcc/10.2.1 || true"
time = { 1.h * task.attempt }
memory = { 30.GB * task.attempt }
cpus = { 5 * task.attempt }
executor = 'sge'
penv = 'smp'
clusterOptions = { '-V -S /bin/bash' }
cache = 'lenient'
// Error handling
errorStrategy = {task.attempt <= 3 ? 'retry' : 'ignore'}
maxRetries = 2
}
withName: colabfold {
time = 10.m
memory = 15.GB
cpus = 1
executor = 'awsbatch'
queue = 'colabfold_spot'
container = "230218818/colabfold"
process.accelerator = 1
process.containerOptions = "--gpus all"
// Error handling
errorStrategy = "ignore"
}
}
//region where we want to run this in
aws.region = 'us-east-1'
// This is the path to the awscli downloaded into the custom AMI
aws.batch.cliPath = '/home/ec2-user/miniconda/bin/aws'
// The custom AMI has the colabfold params copied to /home/ec2-user/params
// This setting mounts that directory to the docker container
aws.batch.volumes = "/home/ec2-user/params:/root/.cache/colabfold"
//============================================================================//
// Misc settings
//============================================================================//
report {
enabled = true
file = "$params.out_dir/nf_information/pipeline_report.html"
}
timeline {
enabled = true
file = "$params.out_dir/nf_information/timeline.html"
}
trace {
enabled = true
file = "$params.out_dir/nf_information/trace.tsv"
}
} // this closes the hybrid profile
biotite {
process {
withName: mmseqs2 {
beforeScript = "module load Sali gcc/10.2.1 || true"
time = { 1.h * task.attempt }
memory = { 30.GB * task.attempt }
cpus = { 5 * task.attempt }
executor = 'slurm'
cache = 'lenient'
// Error handling
errorStrategy = {task.attempt <= 2 ? 'retry' : 'ignore'}
maxRetries = 2
}
withName: colabfold {
time = 2.h
executor = 'slurm'
clusterOptions = { '--gpus 1 --partition gpu' }
process.accelerator = 1
process.containerOptions = "--gpus all"
// Error handling
errorStrategy = {task.attempt <= 2 ? 'retry' : 'ignore'}
maxRetries = 2
}
}
//============================================================================//
// Misc settings
//============================================================================//
report {
enabled = true
file = "$params.out_dir/nf_information/pipeline_report.html"
}
timeline {
enabled = true
file = "$params.out_dir/nf_information/timeline.html"
}
trace {
enabled = true
file = "$params.out_dir/nf_information/trace.tsv"
}
executor {
// Let nextflow submit up to this many jobs in parallel at one time
queueSize = 10
}
} // this closes the biotite profile
lw {
process {
withName: mmseqs2 {
time = { 1.h * task.attempt }
memory = { 30.GB * task.attempt }
cpus = { 5 * task.attempt }
executor = 'slurm'
cache = 'lenient'
// Error handling
errorStrategy = {task.attempt <= 2 ? 'retry' : 'ignore'}
maxRetries = 2
}
withName: colabfold {
time = 2.h
beforeScript = "module load cuda/11.6"
executor = 'slurm'
clusterOptions = { '--account=ac_ribosome --partition=es1 --nodes=1 --ntasks=1 --cpus-per-task=2 --gres=gpu:1 --qos=es_normal --constraint="es1_a40|es1_v100"' }
process.accelerator = 1
process.containerOptions = "--gpus all"
// Error handling
errorStrategy = {task.attempt <= 2 ? 'retry' : 'ignore'}
maxRetries = 2
}
}
//============================================================================//
// Misc settings
//============================================================================//
report {
enabled = true
file = "$params.out_dir/nf_information/pipeline_report.html"
}
timeline {
enabled = true
file = "$params.out_dir/nf_information/timeline.html"
}
trace {
enabled = true
file = "$params.out_dir/nf_information/trace.tsv"
}
executor {
// Let nextflow submit up to this many jobs in parallel at one time
queueSize = 100
}
} // this closes the lw profile
} // This closes the profiles section