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nextflow.config
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/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
nf/pediatric Nextflow config file
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Default config options for all compute environments
----------------------------------------------------------------------------------------
*/
// Global default params, used in configs
params {
// Input options
input = null
//** FreeSurferFlow Options **//
// FastSurfer options
use_fastsurfer = true
fs_license = null
acq3T = true
fs_output_dir = null
// Atlas options
utils_folder = "${projectDir}/assets/FS_BN_GL_SF_utils/"
atlas_name = "BrainnetomeChild"
//** T1 Preprocessing options **//
// Denoising
t1_denoise_number_of_coils = 1
// N4
t1_bias_bspline_knot_per_voxel = 1
t1_bias_shrink_factor = 1
// Resample
t1_resample_voxel_size = 1
t1_resample_interp = "lin"
// Brain extraction
// Synthstrip
t1_run_synthstrip = false
t1_synthstrip_border = 1
t1_synthstrip_nocsf = false
t1_synthstrip_weights = null
// AntsBet
t1_bet_template = "${projectDir}/assets/templates/t1_template.nii.gz"
t1_bet_template_probability_map = "${projectDir}/assets/templates/t1_brain_probability_map.nii.gz"
//** DWI Preprocessing options **//
skip_dwi_preprocessing = false
// Denoising
dwi_denoise_patch_size = 7
// Topup
dwi_susceptibility_config_file = "b02b0.cnf"
dwi_susceptibility_output_prefix = "topup_results"
dwi_susceptibility_readout = 0.040
dwi_susceptibility_b0_threshold = 20
dwi_susceptibility_encoding_dir = "y"
// Eddy
dwi_motion_and_eddy_command = "eddy_cpu"
dwi_motion_and_eddy_bet_f_threshold = 0.16
dwi_motion_and_eddy_restore_slices = true
// Powderaverage
dwi_pwdavg_shells = null
dwi_pwdavg_shell_thr = 50
dwi_pwdavg_b0_thr = 20
// Synthstrip
dwi_run_synthstrip = false
dwi_synthstrip_border = 1
dwi_synthstrip_nocsf = false
dwi_synthstrip_weights = null
// FSL bet
dwi_bet_f_threshold = 0.16
dwi_bet_b0_threshold = 20
// N4
dwi_bias_bspline_knot_per_voxel = 0.25
dwi_bias_shrink_factor = 4
// Normalize
dwi_normalize_fa_mask_threshold = 0.4
dwi_normalize_shell_tolerance = 50
// Resample DWI
dwi_resample_voxel_size = 1
dwi_resample_interp = "lin"
// Extract B0
dwi_extract_b0_threshold = 20
// Resample mask
dwi_resample_mask_voxel_size = 1
dwi_resample_mask_interp = "nn"
//** Reconstruction options **//
// DTI Metrics
dti_shell_tolerance = 50
dti_max_shell_value = 1500
dti_b0_threshold = 20
dti_shells = null
// FRF
frf_fa = 0.7
frf_min_fa = 0.5
frf_nvox_min = 300
frf_roi_radius = 20
frf_dwi_shell_tolerance = 50
frf_max_dti_shell_value = 1500
frf_min_fodf_shell_value = 100
frf_b0_threshold = 20
frf_set_method = "ssst"
frf_set_frf = true
frf_manual_frf = "15,4,4"
frf_mean_frf = false
// FODF Metrics
fodf_shell_tolerance = 50
fodf_min_fodf_shell_value = 100
fodf_shells = null
fodf_b0_threshold = 20
fodf_sh_order = 8
fodf_sh_basis = "descoteaux07"
fodf_set_method = "ssst"
fodf_relative_threshold = 0.1
fodf_a_factor = 2.0
fodf_max_fa_threshold = 0.1
fodf_min_md_threshold = 0.003
// ** Registration options ** //
// Apply registration
reg_dimensionality = 3
reg_interpolation = "NearestNeighbor"
reg_output_dtype = "int"
// ** Tracking options ** //
// PFT Tracking
run_pft_tracking = true
pft_fa_threshold = 0.2
pft_seeding_mask_type = "wm"
pft_random_seed = 1234
pft_compress = true
pft_compress_value = 0.2
pft_algo = "prob"
pft_nbr_seeds = 10
pft_seeding_type = "npv"
pft_step = 0.5
pft_theta = 20
pft_sfthres = 0.1
pft_sfthres_init = 0.5
pft_min_len = 20
pft_max_len = 200
pft_particles = 15
pft_back = 2
pft_front = 1
pft_sh_basis = "descoteaux07"
// Local Tracking
run_local_tracking = true
local_fa_tracking_mask_threshold = 0.4
local_fa_seeding_mask_threshold = 0.4
local_seeding_mask_type = "wm"
local_tracking_mask_type = "wm"
local_random_seed = 1234
local_compress = true
local_compress_value = 0.2
local_algo = "prob"
local_nbr_seeds = 10
local_seeding_type = "npv"
local_step = 0.5
local_theta = 20
local_sfthres = 0.1
local_min_len = 20
local_max_len = 200
local_sh_basis = "descoteaux07"
// ** Connectomics Options ** //
// Transform labels options
labels_transform_dimensionality = 3
labels_interpolation = "NearestNeighbor"
labels_output_dtype = "int"
labels_output_suffix = "_labels"
// COMMIT options
run_commit2 = true
commit2_lambda = 0.001
commit_para_diff = null
commit_iso_diff = null
commit_perp_diff = null
commit_ball_stick = false
commit_nbr_dir = 500
commit_shell_tolerance = 20
// Decompose Options
decompose_no_pruning = false
decompose_no_remove_loops = false
decompose_no_remove_outliers = false
decompose_no_remove_curv = false
decompose_min_len = 20
decompose_max_len = 200
decompose_outlier_threshold = 0.6
decompose_max_angle = 330.0
decompose_max_curv = 10.0
// AFD_Fixel Options
afd_fixel_sh_basis = "descoteaux07"
afd_fixel_length_weighting = false
// MultiQC options
multiqc_config = null
multiqc_title_subject = "nf-pediatric MultiQC Subject Report"
multiqc_title_global = "nf-pediatric MultiQC Global Report"
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
help_full = false
show_hidden = false
version = false
pipelines_testdata_base_path = null
// 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
// Profiles options
infant = false
tracking = false
connectomics = false
freesurfer = false
// Lean output mode.
lean_output = true
// Schema validation default options
validate_params = true
}
// Load base.config by default for all pipelines
includeConfig 'conf/base.config'
profiles {
debug {
dumpHashes = true
process.beforeScript = 'echo $HOSTNAME'
cleanup = false
nextflow.enable.configProcessNamesValidation = true
}
conda {
conda.enabled = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
conda.channels = ['conda-forge', 'bioconda']
apptainer.enabled = false
}
mamba {
conda.enabled = true
conda.useMamba = true
docker.enabled = false
singularity.enabled = false
podman.enabled = false
shifter.enabled = false
charliecloud.enabled = false
apptainer.enabled = false
}
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)'
}
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
}
wave {
apptainer.ociAutoPull = true
singularity.ociAutoPull = true
wave.enabled = true
wave.freeze = true
wave.strategy = 'conda,container'
}
gitpod {
executor.name = 'local'
executor.cpus = 4
executor.memory = 8.GB
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
no_symlink {
params.publish_dir_mode = 'copy'
}
slurm {
process {
maxRetries = 1
cache = "lenient"
afterScript = "sleep 60"
}
executor {
name = 'slurm'
queueSize = 1000
queueGlobalStatus = false
queueStatInterval = '3 min'
submitRateLimit = '10/1sec'
exitReadTimeout = '30 min'
pollInterval = '30 sec'
jobName = {
task.name
.replace("[", "(")
.replace("]", ")")
.replace(" ", "_")
}
}
}
infant {
params.infant = true
params.dwi_run_synthstrip = true
params.dwi_normalize_fa_mask_threshold = 0.10
params.frf_manual_frf = "12,5,5"
params.run_pft_tracking = false
params.local_min_len = 15
params.local_fa_seeding_mask_threshold = 0.10
params.commit_para_diff = "1.2E-3"
params.commit_iso_diff = "2.0E-3"
params.decompose_min_len = 10
params.decompose_outlier_threshold = 0.4
}
tracking {
params.tracking = true
}
connectomics {
params.connectomics = true
}
freesurfer {
params.freesurfer = true
}
}
// Load modules.config for DSL2 module specific options
includeConfig 'conf/modules.config'
// Load nf-core custom profiles from different Institutions
includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null"
// Load nf/pediatric custom profiles from different institutions.
// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/pediatric.config" : "/dev/null"
// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = 'docker.io'
docker.registry = 'docker.io'
podman.registry = 'quay.io'
singularity.registry = 'docker.io'
charliecloud.registry = 'quay.io'
// 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"
}
// Set bash options
process.shell = """\
bash
set -e # Exit if a tool returns a non-zero status/exit code
set -u # Treat unset variables and parameters as an error
set -o pipefail # Returns the status of the last command to exit with a non-zero status or zero if all successfully execute
set -C # No clobber - prevent output redirection from overwriting files.
"""
// 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/pediatric'
author = """Anthony Gagnon"""
homePage = 'https://github.com/nf/pediatric'
description = """nf-pediatric is a neuroimaging pipeline to process pediatric MRI data (including fMRI, dMRI, and sMRI) ranging from 0-18 years old."""
mainScript = 'main.nf'
nextflowVersion = '!>=24.10.0'
version = '1.0dev'
doi = ''
}
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}
validation {
defaultIgnoreParams = ["genomes"]
help {
enabled = true
command = "nextflow run $manifest.name -profile <docker/singularity/.../institute> --input samplesheet.csv --outdir <OUTDIR>"
fullParameter = "help_full"
showHiddenParameter = "show_hidden"
}
}