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profiles.config
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profiles {
conda {
conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
docker {
docker.enabled = true
docker.sudo = false
docker.runOptions = "-u \$(id -u):\$(id -g) --platform=linux/amd64"
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
dev_zeiss_3d {
params.input_dir = "/large_storage/multiomics/projects/lizard_wizard/test_data/zeiss-3d/2024-04-17/Baseline"
params.output_dir = "/large_storage/multiomics/projects/lizard_wizard/test_output/zeiss-3d/"
params.file_type = "zeiss"
params.test_image_names = "2024_04_17_SpheroidCalciumImaging_Baseline-01(1),2024_04_17_SpheroidCalciumImaging_Baseline-01(2)"
params.llm = "gpt-4o-mini"
}
dev_moldev_3d {
params.input_dir = "/large_storage/multiomics/projects/lizard_wizard/test_data/moldev-3d/Calcium_AAV-GCAMP_6wk_20240416/10xGCaMP-6wk-Baseline-Stream/80"
params.output_dir = "/large_storage/multiomics/projects/lizard_wizard/test_output/moldev-3d/"
params.file_type = "moldev"
params.test_image_names = "10xGCaMP-6wk-Baseline-Stream_Stream_F08_s1_FITC,10xGCaMP-6wk-Baseline-Stream_Stream_D10_s1_FITC"
params.llm = "gpt-4o-mini"
}
dev_moldev_2d {
params.input_dir = "/large_storage/multiomics/projects/lizard_wizard/test_data/moldev-2d/Jay"
params.output_dir = "/large_storage/multiomics/projects/lizard_wizard/test_output/moldev-2d/"
params.file_type = "moldev"
params.test_image_names = "20240628- 5wk CoCul B-D 4AP aB_Stream_B08_s3_FITC,20240628- 5wk CoCul B-D 4AP aB_Stream_B08_s1_FITC"
params.use_2d = true
params.llm = "gpt-4o-mini"
}
dev_moldev_2d_sim {
params.output_dir = "/large_storage/multiomics/projects/lizard_wizard/test_output/moldev-2d_sim"
params.file_type = "moldev"
params.simulate = true
params.llm = "gpt-4o-mini"
}
chimera {
workDir = getWorkDir()
conda.cacheDir = getCondaCacheDir()
cache = "lenient"
}
vm {
process.errorStrategy = "terminate"
process.maxRetries = 0
params.max_cpus = 24
params.max_memory = "64.GB"
params.max_time = "72.h"
}
slurm {
process.executor = "slurm"
process.queue = "cpu_batch"
process.errorStrategy = "retry" // "terminate"
process.maxRetries = 2
executor.queueSize = 200
params.max_cpus = 80
params.max_memory = "900.GB"
params.max_time = "48.h"
}
gcp {
workDir = "gs://arc-genomics-nextflow/work"
process.executor = "google-batch"
process.errorStrategy = "retry"
process.maxRetries = 3
process.scratch = true
params.max_cpus = 36
params.max_memory = "800.GB"
params.max_time = "72.h"
google.project = "arc-genomics"
google.location = "us-west1"
}
report {
report.enabled = true
report.overwrite = true
report.file = "${params.output_dir}/nf-report/${params.timestamp}.html"
}
trace {
trace.enabled = true
trace.overwrite = true
trace.file = "${params.output_dir}/nf-trace/${params.timestamp}.txt"
trace.fields = "task_id,hash,native_id,name,status,exit,submit,container,cpus,time,disk,memory,attempt,submit,duration,realtime,%cpu,peak_rss,peak_vmem,rchar,wchar,workdir,scratch"
}
}