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main.nf
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#!/usr/bin/env nextflow
import groovy.json.JsonOutput
nextflow.enable.dsl=2
params.help = false
// ** Importing modules and processes ** //
include { fetch_id;
get_data_freesurfer;
get_data_tracking;
get_data_tracking_infant;
get_data_connectomics;
get_data_connectomics_infant;
get_data_template;
display_run_info } from "./modules/io.nf"
include { DWI;
ANAT } from "./modules/tracking/workflows/preprocessing.nf"
include { DTI } from "./modules/tracking/workflows/DTI.nf"
include { SH } from "./modules/tracking/workflows/SH.nf"
include { REGISTRATION } from "./modules/tracking/workflows/registration.nf"
include { FODF } from "./modules/tracking/workflows/FODF.nf"
include { TRACKING } from "./modules/tracking/workflows/tracking.nf"
include { CONNECTOMICS } from "./modules/connectomics/workflows/connectomics.nf"
include { POPULATION_TEMPLATE } from "./modules/template/workflows/pop_template.nf"
include { FREESURFERFLOW } from "./modules/freesurfer/workflows/freesurferflow.nf"
include { PRIORS } from "./modules/priors/workflows/priors.nf"
workflow {
if (params.help) { display_usage() }
else {
display_run_info()
// ** Checking compatibility between profiles. ** //
if ( params.infant_config && params.run_freesurfer ) {
error "Profiles infant_config and freesurfer are not compatible since infant_freesurfer is not implemented."
}
if ( params.template_config ) {
data = get_data_template()
POPULATION_TEMPLATE(data.anat,
data.dwi,
data.fa,
data.anat_ref,
data.fa_ref)
}
if ( params.run_freesurfer ) {
data = get_data_freesurfer()
utils = Channel.fromPath(params.atlas_utils_folder)
FREESURFERFLOW(data.anat, utils)
}
if ( params.priors && !params.run_tracking ) {
data = get_data_tracking()
PRIORS(data.dwi)
}
if ( params.run_tracking ) {
if ( params.infant_config ) {
data = get_data_tracking_infant()
} else {
data = get_data_tracking()
}
// ** Merging mask and anat if -profile infant. ** //
if ( params.infant_config ) {
anat_channel = data.anat
.combine(data.wm_mask, by: 0)
}
else {
anat_channel = data.anat
}
// ** Anatomical preprocessing ** //
ANAT(anat_channel)
// ** DWI preprocessing ** //
DWI(data.dwi,
data.rev)
// ** DTI modelling ** //
DTI(DWI.out.dwi_bval_bvec,
DWI.out.b0_and_mask)
// ** SH fitting if set ** //
if ( params.sh_fitting ) {
SH(DWI.out.dwi_bval_bvec)
}
// ** Registration of anatomical volume on diffusion volumes. ** //
REGISTRATION(DTI.out.fa_and_md,
ANAT.out.anat_and_mask,
DWI.out.b0_and_mask.map{ [it[0], it[1]] })
// ** Extracting b0 ** //
b0_mask_channel = DWI.out.b0_and_mask
.map{[it[0], it[2]]}
// ** Modelling FODF ** //
FODF(DWI.out.dwi_bval_bvec,
b0_mask_channel,
DTI.out.fa_and_md)
// ** FA channel for tracking maps ** //
fa_channel = DTI.out.fa_and_md
.map{[it[0], it[1]]}
// ** Tracking ** //
TRACKING(REGISTRATION.out.warped_anat,
FODF.out.fodf,
fa_channel)
}
if ( params.priors && params.run_tracking ) {
data = get_data_tracking()
PRIORS(DWI.out.dwi_bval_bvec)
}
if ( params.run_connectomics && params.run_tracking ) {
// ** Fetch tracking data ** //
tracking = TRACKING.out.trk
// ** Fetching labels from freesurferflow if -profile freesurfer is used, if not, ** //
// ** fetching it from input files. ** //
input = file(params.input)
if ( !params.run_freesurfer ) {
labels = Channel.fromFilePairs("$input/**/*labels.nii.gz", size: 1, flat: true)
{ fetch_id(it.parent, input) }
} else {
labels = FREESURFERFLOW.out.labels
}
// ** Preparing metrics channel ** //
dwi_peaks = DWI.out.dwi_bval_bvec
.combine(FODF.out.peaks, by: 0)
fodf = FODF.out.fodf
def_metrics = DTI.out.fa_and_md
.combine(DTI.out.ad_and_rd, by: 0)
.combine(FODF.out.afd_and_nufo, by: 0)
.map{ sid, fa, md, ad, rd, afd, nufo -> tuple(sid, [fa, md, ad, rd, afd, nufo])}
.transpose()
if ( file("$input/**/metrics/*.nii.gz") ) {
// ** Default metrics will be used with combined metrics provided in the input folder ** //
provided_metrics = Channel.fromFilePairs("$input/**/metrics/*.nii.gz", size: -1, flat: false)
{ fetch_id(it.parent.parent, input) }
.transpose()
def_metrics = def_metrics
.concat(provided_metrics)
}
// ** Flattening metrics channel ** //
metrics_flat = def_metrics.groupTuple()
// ** Fetching anat ** //
t2w = REGISTRATION.out.warped_anat
.map{ [it[0], it[1]] }
// ** Fetching transformation files ** //
transfos = REGISTRATION.out.transfos
// ** Fetching FA, MD, AD, RD for priors computation ** //
fa_md_ad_rd_channel = DTI.out.fa_and_md
.combine(DTI.out.ad_and_rd, by: 0)
// ** Launching connectomics workflow ** //
CONNECTOMICS(tracking,
labels,
dwi_peaks,
fodf,
metrics_flat,
t2w,
transfos,
fa_md_ad_rd_channel)
}
if ( params.run_connectomics && !params.run_tracking ) {
if ( params.infant_config ) {
data = get_data_connectomics_infant()
} else {
data = get_data_connectomics()
}
if ( params.run_freesurfer ) {
labels = FREESURFERFLOW.out.labels
anat = FREESURFERFLOW.out.t1
} else {
labels = data.labels
anat = data.anat
}
metrics = data.metrics.transpose().groupTuple()
CONNECTOMICS(data.trk,
labels,
data.dwi_peaks,
data.fodf,
metrics,
anat,
data.transfos,
[])
}
}
}
if (!params.help) {
workflow.onComplete = {
jsonStr = JsonOutput.toJson(params)
file("${params.output_dir}/parameters.json").text = JsonOutput.prettyPrint(jsonStr)
log.info "Pipeline completed at : $workflow.complete"
log.info "Execution status : ${ workflow.success ? 'COMPLETED' : 'FAILED'}"
log.info "Execution duration : $workflow.duration"
}
}
def display_usage () {
if (params.run_tracking && !params.infant_config && !params.run_connectomics && !params.run_freesurfer ) {
usage = file("$projectDir/modules/tracking/USAGE")
} else if (params.run_tracking && params.infant_config && !params.run_connectomics && !params.run_freesurfer ) {
usage = file("$projectDir/modules/tracking/USAGE_INFANT")
} else if (params.run_connectomics && !params.infant_config && !params.run_tracking && !params.run_freesurfer ) {
usage = file("$projectDir/modules/connectomics/USAGE")
} else if (params.run_connectomics && params.infant_config && !params.run_tracking && !params.run_freesurfer ) {
usage = file("$projectDir/modules/connectomics/USAGE_INFANT")
} else if ( params.run_tracking && params.run_connectomics && !params.infant_config && !params.run_freesurfer ) {
usage = file("$projectDir/modules/connectomics/USAGE_TRACKING")
} else if ( params.run_tracking && params.run_connectomics && params.infant_config && !params.run_freesurfer ) {
usage = file("$projectDir/modules/connectomics/USAGE_TRACKING_INFANT")
} else if ( params.run_freesurfer && !params.run_tracking && !params.run_connectomics ) {
usage = file("$projectDir/modules/freesurfer/USAGE")
} else if ( params.run_freesurfer && !params.run_tracking && params.run_connectomics ) {
usage = file("$projectDir/modules/freesurfer/USAGE_CONN")
} else if ( params.run_freesurfer && params.run_tracking && params.run_connectomics ) {
usage = file("$projectDir/modules/connectomics/USAGE_ALL")
} else {
usage = file("$projectDir/USAGE")
}
cpu_count = Runtime.runtime.availableProcessors()
bindings = ["b0_thr":"$params.b0_thr",
"skip_dwi_preprocessing":"$params.skip_dwi_preprocessing",
"initial_bet_f":"$params.initial_bet_f",
"final_bet_f":"$params.final_bet_f",
"run_bet_anat":"$params.run_bet_anat",
"bet_anat_f":"$params.bet_anat_f",
"topup_config":"$params.topup_config",
"encoding_direction":"$params.encoding_direction",
"readout":"$params.readout",
"topup_prefix":"$params.topup_prefix",
"eddy_cmd":"$params.eddy_cmd",
"topup_bet_f":"$params.topup_bet_f",
"use_slice_drop_correction":"$params.use_slice_drop_correction",
"run_synthbet":"$params.run_synthbet",
"shells":"$params.shells",
"shell_thr":"$params.shell_thr",
"gpu":"$params.gpu",
"border":"$params.border",
"nocsf":"$params.nocsf",
"weights":"$params.weights",
"dwi_shell_tolerance":"$params.dwi_shell_tolerance",
"fa_mask_threshold":"$params.fa_mask_threshold",
"anat_resolution":"$params.anat_resolution",
"anat_interpolation":"$params.anat_interpolation",
"mask_interpolation":"$params.mask_interpolation",
"template_t1":"$params.template_t1",
"dwi_resolution":"$params.dwi_resolution",
"dwi_interpolation":"$params.dwi_interpolation",
"mask_dwi_interpolation":"$params.mask_dwi_interpolation",
"dti_shells":"$params.dti_shells",
"max_dti_shell_value":"$params.max_dti_shell_value",
"sh_fitting":"$params.sh_fitting",
"sh_fitting_order":"$params.sh_fitting_order",
"sh_fitting_basis":"$params.sh_fitting_basis",
"fodf_shells":"$params.fodf_shells",
"min_fodf_shell_value":"$params.min_fodf_shell_value",
"fodf_metrics_a_facotr":"$params.fodf_metrics_a_factor",
"max_fa_in_ventricle":"$params.max_fa_in_ventricle",
"min_md_in_ventricle":"$params.min_md_in_ventricle",
"relative_threshold":"$params.relative_threshold",
"basis":"$params.basis",
"sh_order":"$params.sh_order",
"mean_frf":"$params.mean_frf",
"fa":"$params.fa",
"min_fa":"$params.min_fa",
"min_nvox":"$params.min_nvox",
"roi_radius":"$params.roi_radius",
"set_frf":"$params.set_frf",
"manual_frf":"$params.manual_frf",
"number_of_tissues":"$params.number_of_tissues",
"run_pft_tracking":"$params.run_pft_tracking",
"pft_compress_streamlines":"$params.pft_compress_streamlines",
"pft_seeding_mask_type":"$params.pft_seeding_mask_type",
"pft_fa_seeding_mask_thr":"$params.pft_fa_seeding_mask_thr",
"pft_algo":"$params.pft_algo",
"pft_nbr_seeds":"$params.pft_nbr_seeds",
"pft_seeding":"$params.pft_seeding",
"pft_step_size":"$params.pft_step_size",
"pft_theta":"$params.pft_theta",
"pft_sfthres":"$params.pft_sfthres",
"pft_sfthres_init":"$params.pft_sfthres_init",
"pft_min_len":"$params.pft_min_len",
"pft_max_len":"$params.pft_max_len",
"pft_particles":"$params.pft_particles",
"pft_back":"$params.pft_back",
"pft_front":"$params.pft_front",
"pft_compress_value":"$params.pft_compress_value",
"pft_random_seed":"$params.pft_random_seed",
"run_local_tracking":"$params.run_local_tracking",
"local_compress_streamlines":"$params.local_compress_streamlines",
"local_fa_seeding_mask_thr":"$params.local_fa_seeding_mask_thr",
"local_seeding_mask_type":"$params.local_seeding_mask_type",
"local_fa_tracking_mask_thr":"$params.local_fa_tracking_mask_thr",
"local_tracking_mask_type":"$params.local_tracking_mask_type",
"local_algo":"$params.local_algo",
"local_seeding":"$params.local_seeding",
"local_nbr_seeds":"$params.local_nbr_seeds",
"local_tracking_seed":"$params.local_tracking_seed",
"local_step_size":"$params.local_step_size",
"local_theta":"$params.local_theta",
"local_sfthres":"$params.local_sfthres",
"local_sfthres_init":"$params.local_sfthres_init",
"local_min_len":"$params.local_min_len",
"local_max_len":"$params.local_max_len",
"local_erosion":"$params.local_erosion",
"local_compress_value":"$params.local_compress_value",
"output_dir":"$params.output_dir",
"processes_denoise_dwi":"$params.processes_denoise_dwi",
"processes_denoise_t1":"$params.processes_denoise_t1",
"processes_bet_t1":"$params.processes_bet_t1",
"processes_eddy":"$params.processes_eddy",
"processes_registration":"$params.processes_registration",
"processes_fodf":"$params.processes_fodf",
"no_pruning":"$params.no_pruning",
"no_remove_loops":"$params.no_remove_loops",
"no_remove_outliers":"$params.no_remove_outliers",
"min_length":"$params.min_length",
"max_length":"$params.max_length",
"loop_max_angle":"$params.loop_max_angle",
"outlier_threshold":"$params.outlier_threshold",
"compute_priors":"$params.compute_priors",
"fa_min_priors":"$params.fa_min_priors",
"fa_max_priors":"$params.fa_max_priors",
"md_min_priors":"$params.md_min_priors",
"roi_radius_priors":"$params.roi_radius",
"run_commit":"$params.run_commit",
"use_commit2":"$params.use_commit2",
"use_both_commit":"$params.use_both_commit",
"commit_on_trk":"$params.commit_on_trk",
"b_thr":"$params.b_thr",
"ball_stick":"$params.ball_stick",
"nbr_dir":"$params.nbr_dir",
"para_diff":"$params.para_diff",
"perp_diff":"$params.perp_diff",
"iso_diff":"$params.iso_diff",
"processes_commit":"$params.processes_commit",
"processes_afd_fixel":"$params.processes_afd_fixel",
"processes_connectivity":"$params.processes_connectivity",
"references":"$params.references",
"recon_all":"$params.recon_all",
"recon_surf":"$params.recon_surf",
"use_freesurfer_atlas":"$params.use_freesurfer_atlas",
"use_brainnetome_atlas":"$params.use_brainnetome_atlas",
"use_brainnetome_child_atlas":"$params.use_brainnetome_child_atlas",
"use_glasser_atlas":"$params.use_glasser_atlas",
"use_schaefer_100_atlas":"$params.use_schaefer_100_atlas",
"use_schaefer_200_atlas":"$params.use_schaefer_200_atlas",
"use_schaefer_400_atlas":"$params.use_schaefer_400_atlas",
"use_lausanne_1_atlas":"$params.use_lausanne_1_atlas",
"use_lausanne_2_atlas":"$params.use_lausanne_2_atlas",
"use_lausanne_3_atlas":"$params.use_lausanne_3_atlas",
"use_lausanne_4_atlas":"$params.use_lausanne_4_atlas",
"use_lausanne_5_atlas":"$params.use_lausanne_5_atlas",
"use_dilated_labels":"$params.use_dilated_labels",
"nb_threads":"$params.nb_threads",
"atlas_utils_folder":"$params.atlas_utils_folder",
"compute_FS_BN_GL_SF":"$params.compute_FS_BN_GL_SF",
"compute_BN_child":"$params.compute_BN_child",
"compute_lausanne_multiscale":"$params.compute_lausanne_multiscale",
"compute_lobes":"$params.compute_lobes",
"run_freesurfer":"$params.run_freesurfer",
"run_tracking":"$params.run_tracking",
"run_connectomics":"$params.run_connectomics",
"template_config":"$params.template_config",
"processes":"$params.processes",
"cpu_count":"$cpu_count"
]
engine = new groovy.text.SimpleTemplateEngine()
template = engine.createTemplate(usage.text).make(bindings)
print template.toString()
}