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nextflow.config
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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf/tractoflow Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
//*BIDS options**//
clean_input_bids = false
//**Surgeryflow parameters**//
run_synthbet = true
run_synthseg = true
run_synthmorph = true
//**Freesurfer license**//
fs_license = "license.txt"
//**Global options**//
dwi_b0_extract_threshold = 10
dwi_shell_extract_tolerance = 20
//**SH fitting**//
dwi_fit_signal_sh = true //FIXME
dwi_signal_sh_fit_order = 6 //FIXME
dwi_signal_sh_fit_basis = "descoteaux07" //FIXME
dwi_signal_sh_fit_shell = null //FIXME
//**Preliminary DWI brain extraction**//
dwi_mask_prelim_bet_dilation_radius = 5
dwi_mask_prelim_bet_f_threshold = 0.16
//**Denoise dwi (dwidenoise in Mrtrix3)**//
dwi_filter_noise = true //FIXME
dwi_noise_filter_patch_size = 7
//**GIBBS CORRECTION (mrdegibbs in Mrtrix3)**//
dwi_filter_gibbs = false //FIXME
//**Topup**//
dwi_filter_susceptibility = true //FIXME
dwi_susceptibility_filter_config_file = "b02b0.cnf"
dwi_susceptibility_filter_output_prefix = "topup_results"
//**Eddy**//
dwi_filter_eddy_and_motion = false //FIXME
dwi_motion_and_eddy_filter_command = "eddy_cpu"
dwi_motion_and_eddy_filter_bet_f_threshold = 0.16
dwi_motion_and_eddy_filter_restore_slices = true
//**N4 bias correction**//
dwi_bias_correction_bspline_knots_per_voxel = 0.25
dwi_bias_correction_shrink_factor = 4
//**Final DWI BET**//
dwi_mask_final_bet_f_threshold = 0.16
//**Denoise T1**//
t1_filter_noise = true //FIXME
//* T1 BET**//
t1_bet_template_t1 = "/human-data/mni_152_sym_09c/t1/t1_template.nii.gz"
t1_bet_template_probability_map = "/human-data/mni_152_sym_09c/t1/t1_brain_probability_map.nii.gz"
t1_bet_no_csf = true
//**Resample T1**//
t1_resample_spatial = true //FIXME
t1_spatial_resample_resolution = 1
t1_spatial_resample_interpolation = "lin"
//**Register T1**//
t1_register_field = true
t1_register_fs_license = "license.txt"
t1_register_synthmorph_regularization = 0.5
//**Normalize DWI**//
dwi_intensities_normalize_fa_mask_threshold = 0.4 //FIXME
//**Resample DWI**//
dwi_resample_spatial = true //FIXME
dwi_spatial_resample_resolution = 1
dwi_spatial_resample_interpolation = "lin"
//**Extract DTI shells using this value as maximum**//
dwi_dti_fit_shell_max_bvalue = 1200 //FIXME
dwi_dti_fit_shells = null //FIXME
//**Extract fODF shells using this value as minimum**//
dwi_fodf_fit_shell_min_bvalue = 700
dwi_fodf_fit_shells = null
//**Segment tissues**//
t1_tissue_segment_n_classes = 3 //FIXME
t1_tissue_segment_synth_fast = true
//**Compute fiber response function (frf)**//
dwi_fodf_fit_frf_max_fa_threshold = 0.7
dwi_fodf_fit_frf_min_fa_threshold = 0.5
dwi_fodf_fit_frf_min_n_voxels = 300
dwi_fodf_fit_frf_roi_radius = 20
dwi_fodf_fit_force_frf = null
//**Mean fiber response function (frf)**//
dwi_fodf_fit_use_average_frf = false //FIXME
//**Compute fODF metrics**//
dwi_fodf_fit_order = 8
dwi_fodf_fit_basis = "descoteaux07"
dwi_fodf_fit_peaks_absolute_factor = 2.0
dwi_fodf_fit_peaks_relative_threshold = 0.1
dwi_fodf_fit_peaks_ventricle_max_fa = 0.1
dwi_fodf_fit_peaks_ventricle_min_md = 0.003
//**PFT tracking**//
fodf_fit_pft = true
fodf_pft_fit_random_seed = 0
fodf_pft_fit_algorithm = "prob"
fodf_pft_fit_step_size = 0.5
fodf_pft_fit_theta_max_deviation = 20
fodf_pft_fit_streamline_min_length = 20
fodf_pft_fit_streamline_max_length = 200
fodf_pft_fit_seeding_type = "wm"
fodf_pft_fit_seeding_strategy = "npv"
fodf_pft_fit_seeding_n_seeds = 10
fodf_pft_fit_seeding_fa_mask_threshold = 0.1
fodf_pft_fit_filter_n_particles = 15
fodf_pft_fit_filter_backward_step_size = 2
fodf_pft_fit_filter_forward_step_size = 1
fodf_pft_fit_sf_threshold = 0.1
fodf_pft_fit_sf_initial_threshold = 0.5
fodf_pft_fit_compress_tractogram = true
fodf_pft_fit_compress_max_displacement = 0.2
//**Local tracking**//
fodf_fit_local = false
fodf_local_fit_processor = "cpu" //FIXME
fodf_local_fit_gpu_batch_size = 10000 //FIXME
fodf_local_fit_random_seed = 0
fodf_local_fit_algorithm = "prob"
fodf_local_fit_step_size = 0.5
fodf_local_fit_theta_max_deviation = 20
fodf_local_fit_streamline_min_length = 20
fodf_local_fit_streamline_max_length = 200
fodf_local_fit_seeding_type = "wm"
fodf_local_fit_seeding_strategy = "npv"
fodf_local_fit_seeding_n_seeds = 10
fodf_local_fit_seeding_fa_threshold = 0.1
fodf_local_fit_tracking_mask_type = "wm"
fodf_local_fit_tracking_mask_fa_threshold = 0.1
fodf_local_fit_sf_threshold = 0.1
fodf_local_fit_sf_initial_threshold = 0.5 //FIXME
fodf_local_fit_compress_tractogram = true
fodf_local_fit_compress_max_displacement = 0.2
//**Bundle segmentation**//
bundle_atlas_directory = "/path/to/atlas_directory"
bundle_rbx_seed = 0
bundle_rbx_outlier_alpha = 0.5
bundle_rbx_minimal_vote_ratio = 0.1
//**Processes Maximum CPU allocation**//
allocation_cpu_max_bet = 4 //FIXME
allocation_cpu_max_dwi_filter_noise = 4 //FIXME
allocation_cpu_max_dwi_filter_motion_and_eddy = 4 //FIXME
allocation_cpu_max_dwi_fit_fodf = 4 //FIXME
allocation_cpu_max_fodf_fit_local = 4 //FIXME
allocation_cpu_max_t1_filter_noise = 4 //FIXME
allocation_cpu_max_t1_registration = 4 //FIXME
allocation_cpu_map_bundle_register = 4 //FIXME
allocation_cpu_map_bundle_rbx = 4 //FIXME
// Input options
input = null// MultiQC options
bids = null
multiqc_config = null
multiqc_title = null
multiqc_logo = null
max_multiqc_email_size = '25.MB'
multiqc_methods_description = null
// Boilerplate options
outdir = null
publish_dir_mode = 'copy'
email = null
email_on_fail = null
plaintext_email = false
monochrome_logs = false
hook_url = null
help = false
version = false
//TODO: RBX head params?
root = false
// Config options
config_profile_name = null
config_profile_description = null
custom_config_version = 'master'
custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
config_profile_contact = null
config_profile_url = null
// Max resource options
// Defaults only, expecting to be overwritten
max_memory = '24.GB'
max_cpus = 16
max_time = '240.h'
// Schema validation default options
validationFailUnrecognisedParams = false
validationLenientMode = false
validationSchemaIgnoreParams = 'genomes,igenomes_base'
validationShowHiddenParams = false
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
// Load nf-core custom profiles from different Institutions
try {
includeConfig "${params.custom_config_base}/nfcore_custom.config"
} catch (Exception e) {
System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
}
// Load nf/tractoflow custom profiles from different institutions.
// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs!
// try {
// includeConfig "${params.custom_config_base}/pipeline/tractoflow.config"
// } catch (Exception e) {
// System.err.println("WARNING: Could not load nf-core/config/tractoflow profiles: ${params.custom_config_base}/pipeline/tractoflow.config")
// }
profiles {
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
nextflow.enable.configProcessNamesValidation = true
}
docker {
docker.enabled = true
conda.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
docker.runOptions = '-u $(id -u):$(id -g)'
docker.runOptions = "--user root"
}
arm {
docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
}
singularity {
singularity.enabled = true
singularity.autoMounts = true
conda.enabled = false
docker.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
podman {
podman.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
shifter {
shifter.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
charliecloud {
charliecloud.enabled = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
apptainer.enabled = false
}
apptainer {
apptainer.enabled = true
apptainer.autoMounts = true
conda.enabled = false
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
}
gitpod {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
}
fully_reproductible {
params.allocation_cpu_map_bundle_register = 4
params.allocation_cpu_map_bundle_rbx = 4
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
}
// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = 'quay.io'
docker.registry = 'docker.io'
podman.registry = 'quay.io'
singularity.registry = 'quay.io'
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
// Capture exit codes from upstream processes when piping
process.shell = ['/bin/bash', '-euo', 'pipefail']
// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false
def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
}
manifest {
name = 'nf/surgeryflow'
author = """@AlexVCaron"""
homePage = 'https://github.com/nf/surgeryflow'
description = """Human diffusion MRI processing and tractography for neurosurgery"""
mainScript = 'main.nf'
nextflowVersion = '!>=23.04.0'
version = '1.0dev'
doi = ''
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Function to ensure that resource requirements don't go beyond
// a maximum limit
def check_max(obj, type) {
if (type == 'memory') {
try {
if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
return params.max_memory as nextflow.util.MemoryUnit
else
return obj
} catch (all) {
println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'time') {
try {
if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
return params.max_time as nextflow.util.Duration
else
return obj
} catch (all) {
println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj"
return obj
}
} else if (type == 'cpus') {
try {
return Math.min( obj, params.max_cpus as int )
} catch (all) {
println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
return obj
}
}
}