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nextflow.config
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880 lines (812 loc) · 33.5 KB
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includeConfig 'conf/base.config'
// Global default params, used in configs
params {
// Mandatory arguments
input = false
// Output
outdir = 'results_mouse'
// Denoising
run_denoising = true
// Eddy
run_eddy = true
processes = 10
// N4
run_n4 = true
// Resampling
run_resampling = true
// DTI
max_dti_shell_value = 3500
// FRF
nvox_min = 100
// FODF || QBALL
use_fodf_for_tracking = false
sh_order = 6
min_fodf_value = 1000
// Tracking
run_tracking = true
local_nbr_seeds=1
local_step_pct=50
local_theta=45
local_rk_order=1
local_min_len=3
local_max_len=12
local_algo = "det"
lean_output = true
use_gpu = false
// General params
b0_threshold = 100
shell_tolerance = 100
// pre_qc
run_preqc = false
use_preqc = false
trace_report_suffix = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')// Config options
}
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
process {
resourceLimits = [
memory: 8.GB,
cpus : 4,
time : 1.h
]
}
}
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(" ", "_")
}
}
}
slurm_curta {
process {
maxRetries = 1
cache = "lenient"
afterScript = "sleep 60"
resourceLimits = [
cpus: 64,
memory: 3.TB,
time: 720.h]
}
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(" ", "_")
}
}
}
gpu {
params.use_gpu = true
docker.runOptions = '-u $(id -u):$(id -g) --gpus all'
singularity.runOptions='--nv'
apptainer.runOptions='--nv'
}
pre_qc {
params.run_preqc = true
}
}
report.overwrite = true
process {
withName: "PRE_QC" {
ext.b0_thr_extract_b0 = params.b0_threshold
}
withName: "DENOISING_MPPCA" {
ext.extent = 3
publishDir = [
path: { "${params.outdir}/${meta.id}/dwi/"},
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.lean_output ? false : true
]
}
withName: "PREPROC_SINGLEEDDY" {
ext.eddy_cmd = params.use_gpu ? "eddy" : "eddy_cpu"
ext.encoding = "y"
ext.readout = 0.01536
ext.extra_args = ""
ext.extra_ite = 15
ext.extra_thr = params.use_gpu ? 1 : params.processes
publishDir = [
path: { "${params.outdir}/${meta.id}/dwi/"},
saveAs: {
filename ->
if ( filename.contains("bvec") ) { "${meta.id}_desc-preproc_dwi.bvec" }
else if ( filename.contains("bval") ) {"${meta.id}_desc-preproc_dwi.bval"}
else if ( filename.contains("versions.yml") ) { null }
else { params.lean_output ? null : filename }
}
]
}
withName: "UTILS_EXTRACTB0" {
ext.b0_threshold = params.b0_threshold
}
withName: "PREPARE_NNUNET_B0" {
ext.suffix = "b0"
}
withName: "PREPARE_NNUNET_DWI" {
ext.suffix = "dwi"
}
withName: "MOUSE_N4" {
ext.threshold=0.001
ext.convergence = "150x150x150x150"
publishDir = [
path: { "${params.outdir}/${meta.id}/dwi/"},
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.lean_output ? false : true
]
}
withName: "RESAMPLE_DWI" {
ext.iso_min = true
ext.interp = "lin"
publishDir = [
path: { "${params.outdir}/${meta.id}/dwi/"},
saveAs: {
filename ->
if ( filename.contains("_resampled.nii.gz") ) { "${meta.id}_desc-preproc_dwi.nii.gz" }
else if ( filename.contains("versions.yml") ) { null }
else { params.lean_output ? null : filename }
}
]
}
withName: "RESAMPLE_MASK" {
ext.iso_min = true
ext.interp = "nn"
ext.first_suffix = "mask"
publishDir = [
path: { "${params.outdir}/${meta.id}/anat/"},
saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
enabled: params.lean_output ? false : true
]
}
withName: "MOUSE_REGISTRATION" {
ext.laplacian_value = "0.1mm"
ext.atlas_50_resolution = "50"
ext.atlas_100_resolution = "100"
ext.atlas_resolution = ""
ext.run_qc = true
publishDir = [
path: { "${params.outdir}/${meta.id}/anat/"},
saveAs: {
filename ->
if ( filename.contains("ANO.nii.gz") ) { "${meta.id}_atlas-Allen_desc-ANO_dseg.nii.gz"}
else if ( filename.contains("ANO_LR.nii.gz") ) { "${meta.id}_atlas-Allen_desc-ANOLR_dseg.nii.gz"}
else if ( filename.contains("moving_check") ) { "${meta.id}_atlas-Allen_2PE.nii.gz"}
else if ( filename.contains("0GenericAffine.mat") ) { "${meta.id}_from-Allen_to-dwi_affine.mat"}
else if ( filename.contains("1Warp.nii.gz") ) { "${meta.id}_from-Allen_to-dwi_warp.nii.gz"}
else if ( filename.contains("1InverseWarp.nii.gz") ) { "${meta.id}_from-dwi_to-Allen_warp.nii.gz"}
else if ( filename.contains("versions.yml") ) { null }
else { params.lean_output ? null : filename }
}
]
}
withName: "IMAGE_CONVERT" {
ext.datatype = "uint8"
ext.first_suffix = "mask"
publishDir = [
path: { "${params.outdir}/${meta.id}/dwi/"},
saveAs: {
filename ->
if ( filename.contains("_converted.nii.gz") ) { "${meta.id}_desc-preproc_mask.nii.gz" }
else if ( filename.contains("versions.yml") ) { null }
else { params.lean_output ? null : filename }
}
]
}
withName: "MULTIQC" {
publishDir = [
path: { "${params.outdir}/${meta.id}/report/"},
saveAs: {
filename ->
if ( filename.contains("_multiqc_report.html") ) { "${meta.id}_multiqc_report.html" }
else if ( filename.contains("versions.yml") ) { null }
else { params.lean_output ? null : filename }
}
]
}
withName: "RECONST_DTIMETRICS" {
ext.ad = true
ext.evecs = true
ext.evals = true
ext.fa = true
ext.ga = true
ext.rgb = true
ext.md = true
ext.mode = true
ext.norm = true
ext.rd = true
ext.tensor = true
ext.nonphysical = true
ext.pulsation = true
ext.residual = true
ext.b0_thr_extract_b0 = params.b0_threshold
ext.dwi_shell_tolerance = params.shell_tolerance
ext.max_dti_shell_value = params.max_dti_shell_value
ext.run_qc = true
publishDir = [
path: { "${params.outdir}/${meta.id}/dwi/"},
saveAs: {
filename ->
if ( filename.contains("ad.nii.gz") ) { "${meta.id}_model-tensor_param-ad_dwimap.nii.gz" }
else if ( filename.contains("fa.nii.gz") ) { "${meta.id}_model-tensor_param-fa_dwimap.nii.gz" }
else if ( filename.contains("rd.nii.gz") ) { "${meta.id}_model-tensor_param-rd_dwimap.nii.gz" }
else if ( filename.contains("md.nii.gz") ) { "${meta.id}_model-tensor_param-md_dwimap.nii.gz" }
else if ( filename.contains("mode.nii.gz") ) { "${meta.id}_model-tensor_param-mode_dwimap.nii.gz" }
else if ( filename.contains("tensor.nii.gz") ) { "${meta.id}_model-tensor_param-tensor_dwimap.nii.gz" }
else if ( filename.contains("rgb.nii.gz") ) { "${meta.id}_model-tensor_param-rgb_dwimap.nii.gz" }
else if ( filename.contains("ga.nii.gz") ) { "${meta.id}_model-tensor_param-ga_dwimap.nii.gz" }
else if ( filename.contains("mqc.png") ) { "${meta.id}_mqc.png" }
else if ( filename.contains("evecs_v1.nii.gz") ) { "${meta.id}_model-tensor_param-v1_dwimap.nii.gz" }
else if ( filename.contains("evecs_v2.nii.gz") ) { "${meta.id}_model-tensor_param-v2_dwimap.nii.gz" }
else if ( filename.contains("evecs_v3.nii.gz") ) { "${meta.id}_model-tensor_param-v3_dwimap.nii.gz" }
else if ( filename.contains("versions.yml") ) { null }
else { params.lean_output ? null : filename }
}
]
}
withName: "RECONST_FRF" {
ext.nvox_min = params.nvox_min
ext.max_dti_shell_value = params.max_dti_shell_value
}
withName: "RECONST_FODF" {
ext.sh_order = 6
ext.sh_basis = "descoteaux07"
ext.fa_threshold = 0.1
ext.md_threshold = 0.003
ext.relative_threshold = 0.1
ext.absolute_peaks = true
ext.peaks = true
ext.peak_values = true
ext.peak_indices = true
ext.afd_max = true
ext.afd_total = true
ext.afd_sum = true
ext.nufo = true
ext.b0_thr_extract_b0 = params.b0_threshold
ext.min_fodf_shell_value = params.min_fodf_value
publishDir = [
path: { "${params.outdir}/${meta.id}/dwi/"},
saveAs: {
filename ->
if ( filename.contains("fodf.nii.gz") ) { "${meta.id}_model-csd_param-sh_dwimap.nii.gz" }
else if ( filename.contains("wm.nii.gz") ) { "${meta.id}_model-csd_param-wm_dwimap.nii.gz" }
else if ( filename.contains("gm.nii.gz") ) { "${meta.id}_model-csd_param-gm_dwimap.nii.gz" }
else if ( filename.contains("csf.nii.gz") ) { "${meta.id}_model-csd_param-csf_dwimap.nii.gz" }
else if ( filename.contains("vf.nii.gz") ) { "${meta.id}_model-csd_param-vf_dwimap.nii.gz" }
else if ( filename.contains("vf_rgb.nii.gz") ) { "${meta.id}_model-csd_param-rgb_dwimap.nii.gz" }
else if ( filename.contains("afd_total.nii.gz") ) { "${meta.id}_model-csd_param-afdtot_dwimap.nii.gz" }
else if ( filename.contains("afd_sum.nii.gz") ) { "${meta.id}_model-csd_param-afdsum_dwimap.nii.gz" }
else if ( filename.contains("afd_max.nii.gz") ) { "${meta.id}_model-csd_param-afdmax_dwimap.nii.gz" }
else if ( filename.contains("nufo.nii.gz") ) { "${meta.id}_model-csf_csd_param-nufo_dwimap.nii.gz" }
else if ( filename.contains("rgb.nii.gz") ) { "${meta.id}_model-csd_param-rgb_dwimap.nii.gz" }
else if ( filename.contains("peak_indices.nii.gz") ) { "${meta.id}_model-csd_param-peakindices_dwimap.nii.gz" }
else if ( filename.contains("peak_values.nii.gz") ) { "${meta.id}_model-csd_param-peakvalues_dwimap.nii.gz" }
else if ( filename.contains("versions.yml") ) { null }
else { params.lean_output ? null : filename }
}
]
}
withName: "RECONST_QBALL" {
ext.sh_order = params.sh_order
ext.qball = true
ext.gfa = true
ext.a_power = true
ext.nufo = true
ext.peaks = true
publishDir = [
path: { "${params.outdir}/${meta.id}/dwi/"},
saveAs: { filename ->
if ( filename.contains("__qball.nii.gz") ) { "${meta.id}_model-qball_param-sh_dwimap.nii.gz" }
else if ( filename.contains("gfa.nii.gz") ) { "${meta.id}_model-qball_param-gfa_dwimap.nii.gz" }
else if ( filename.contains("a_power.nii.gz") ) { "${meta.id}_model-qball_param-apower_dwimap.nii.gz" }
else if ( filename.contains("nufo.nii.gz") ) { "${meta.id}_model-qball_param-nufo_dwimap.nii.gz" }
else if ( filename.contains("evecs_v1.nii.gz") ) { "${meta.id}_model-qball_param-v1_dwimap.nii.gz" }
else if ( filename.contains("evecs_v2.nii.gz") ) { "${meta.id}_model-qball_param-v2_dwimap.nii.gz" }
else if ( filename.contains("evecs_v3.nii.gz") ) { "${meta.id}_model-qball_param-v3_dwimap.nii.gz" }
else if ( filename.contains("versions.yml") ) { null }
else { params.lean_output ? null : filename }
}
]
}
withName: "TRACKING_MASK" {
ext.ventricules_labels_ids="82 401 748 800 961 962 963 1092 1107 1132 1145 1146"
ext.seeding_labels_ids="1181 1149 1309 1321 405 1240 1216 1214 1215 1123 1119 374 1124 1131 1153 1238 1241 1315 373 1228 1244 403 402 1091 1111 1229 1278 1231 1292 971 1199 1189 970 1160 1317 1133 1307 1201 1161 1213 1147 1130 404 1116 1311 1114 1113 1322 1169 1144 1167 1164 1318 1183 1163 1159 1191 1200 1227 1294 1300 1301 1280 1291 1293 1306 1299 1286 1297 1198 1135 1134 1136 1279 1170 1281 1316 1283 1217 1203 1282 1143 1209 1129 1239 1267 1308 1128 1284 1211 1138 1179 1173 1174 1140 1182 1141 1139 1142 1154 1205 1150 1158 1152 1151 1137 1265 1266 1155 1156 1212 1176 1204 1232 1310 1242 1127 1177 1178 1243 1236 1237 1262 1290 1298 1312 1314 1171 1313 1276 1324 1272 1157 1273 1274 1275 1323 1221 1220 1122 1125 1120 1148 1188 1121 1165 1180 1187 1162 1186 1218 1185 1196 1166 1319 1247 1118 1210 1295 1296 1226 1219 1320 1258 1302 1303 1304 1305 1257 1289 1249 1250 1251 1252 1253 1263 1224 1255 1234 1233 1230 1225 1264 1222 1288 1184 1195 654 1223 1168 1172 1271"
ext.run_qc = true
publishDir = [
path: { "${params.outdir}/${meta.id}/anat/"},
saveAs: {
filename ->
if ( filename.contains("seeding_mask") ) { "${meta.id}_desc-seeding_mask.nii.gz" }
else if ( filename.contains("tracking_mask") ) { "${meta.id}_desc-tracking_mask.nii.gz" }
else if ( filename.contains("versions.yml") ) { null }
else { params.lean_output ? null : filename }
}
]
}
withName: "TRACKING_LOCALTRACKING" {
ext.local_compress_streamlines=false
ext.run_local_tracking=true
ext.local_algo=params.local_algo
ext.local_seeding="npv"
ext.local_nbr_seeds = params.local_nbr_seeds
ext.local_step_pct = params.local_step_pct
ext.local_theta = params.local_theta
ext.local_rk_order = params.local_rk_order
ext.local_min_len = params.local_min_len
ext.local_max_len = params.local_max_len
ext.local_tracking_mask_type="wm"
ext.local_seeding_mask_type="fa"
ext.local_fa_seeding_mask_threshold="0"
ext.local_fa_tracking_mask_threshold="0"
ext.run_qc = true
publishDir = [
path: { "${params.outdir}/${meta.id}/dwi/"},
saveAs: {
filename ->
if ( filename.contains("local_tracking.trk") ) { "${meta.id}_desc-local_tracking.trk" }
else if ( filename.contains("seeding_mask") ) { "${meta.id}_label-seeding_desc-local_mask.nii.gz" }
else if ( filename.contains("tracking_mask") ) { "${meta.id}_label-tracking_desc-local_mask.nii.gz"}
else if ( filename.contains("versions.yml") ) { null }
else { params.lean_output ? null : filename }
}
]
}
withName: "MOUSE_EXTRACTMASKS" {
ext.labels = "ACA AI AOB AON APr AUD BLA BMA CA CBN CBX CLA COA CP DG DP ECT ENT EP FRP GU HATA HY IG ILA LA LSS MB MO MOB MY ORB NLOT P PA PAA PAL PAR PERI PIR PL POST PRE ProS PTLp RSP sAMY SS SUB TEa TH TR TT VIS VIS fiber_tracts cc"
ext.labels_dup = "FRP MO SS GU VISC Tea fiber_tracts"
publishDir = [
path: { "${params.outdir}/${meta.id}/anat/"},
saveAs: {
filename ->
if ( filename.contains("masks") ) { "${meta.id}_masks" }
else { params.lean_output ? null : filename }
}
]
}
withName: "MOUSE_VOLUMEROISTATS" {
publishDir = [
path: { "${params.outdir}/${meta.id}/stats/"},
saveAs: {
filename ->
if ( filename.contains("stats") ) { "${meta.id}__stats.json" }
else { params.lean_output ? null : filename }
}
]
}
withName: "COMBINESTATS_MERGED" {
ext.convert_to_xlsx = true
publishDir = [
path: { "${params.outdir}/stats/"},
saveAs: {
filename ->
if ( filename.contains("stats.json") ) { "all_stats.json" }
else if ( filename.contains("stats.xlsx") ) { "all_stats.xlsx" }
else { params.lean_output ? null : filename }
}
]
}
withName: "STATS_AMBA" {
ext.use_label=true
ext.output_format='csv'
publishDir = [
path: { "${params.outdir}/${meta.id}/stats/"},
saveAs: {
filename ->
if ( filename.contains("mean_stats.csv") ) { "${meta.id}_desc-ANO_stats-mean.csv" }
else if ( filename.contains("std_stats.csv") ) { "${meta.id}_desc-ANO_stats-std.csv" }
else { params.lean_output ? null : filename }
}
]
}
withName: "STATS_AMBA_LR" {
ext.use_label=true
ext.output_format='csv'
publishDir = [
path: { "${params.outdir}/${meta.id}/stats/"},
saveAs: {
filename ->
if ( filename.contains("mean_stats.csv") ) { "${meta.id}_desc-ANOLR_stats-mean.csv" }
else if ( filename.contains("std_stats.csv") ) { "${meta.id}_desc-ANOLR_stats-std.csv" }
else { params.lean_output ? null : filename }
}
]
}
withName: "COMBINESTATS_AMBA" {
ext.convert_to_xlsx = true
ext.key = true
publishDir = [
path: { "${params.outdir}/stats/"},
saveAs: {
filename ->
if ( filename.contains("stats.json") ) { "all_stats_amba.json" }
else if ( filename.contains("stats.xlsx") ) { "all_stats_amba.xlsx" }
else { params.lean_output ? null : filename }
}
]
}
withName: "COMBINESTATS_AMBA_LR" {
ext.convert_to_xlsx = true
ext.key = true
publishDir = [
path: { "${params.outdir}/stats/"},
saveAs: {
filename ->
if ( filename.contains("stats.json") ) { "all_stats_amba_lr.json" }
else if ( filename.contains("stats.xlsx") ) { "all_stats_amba_lr.xlsx" }
else { params.lean_output ? null : filename }
}
]
}
withName: "CREATE_FX_EXCLUDE" {
ext.suffix = "FX_exclude"
ext.labels_ids = "287 288 292 295 297 300 301 304 306 308 1119 1120 1139 1142 1205 1238 1241 1242"
ext.run_qc = true
publishDir = [
path: { "${params.outdir}/${meta.id}/anat/"},
saveAs: {
filename ->
if ( filename.contains("FX_include_mask") ) { "${meta.id}_label-FX_desc-exclude_mask.nii.gz" }
else { params.lean_output ? null : filename }
}
]
}
withName: "CREATE_FX_INCLUDE" {
ext.suffix = "FX_include"
ext.labels_ids = "149 154 159 1121 1180 1185"
ext.run_qc = true
publishDir = [
path: { "${params.outdir}/${meta.id}/anat/"},
saveAs: {
filename ->
if ( filename.contains("FX_include_mask") ) { "${meta.id}_label-FX_desc-include_mask.nii.gz" }
else { params.lean_output ? null : filename }
}
]
}
withName: "CREATE_FX" {
ext.suffix = "FX"
ext.run_qc = true
publishDir = [
path: { "${params.outdir}/${meta.id}/dwi/"},
saveAs: {
filename ->
if ( filename.contains("FX_tracking.trk") ) { "${meta.id}_label-FX_desc-tracking.trk" }
else if ( filename.contains("FX_tracking_stats") ) { "${meta.id}_label-FX_desc-stats.json" }
else { params.lean_output ? null : filename }
}
]
}
withName: "CREATE_CST_EXCLUDE" {
ext.suffix = "CST_exclude"
ext.labels_ids = "1119 1120 1138 1179 1173 1174 1140 1182 1141 1139 1142 167 169 170 168 967 426 428 429 427 175 176 178 179 177 180 182 183 181 223 224 230 231 229 232 234 235 233 225 227 228 226 239 241 242 240 329 331 332 330 730 732 733 731 956 958 959 957 542 544 545 543 355 807 809 810 808 58 59 61 62 60 63 65 66 64 685 687 688 686 211 213 214 212 637 639 640 638 324 326 327 325 166 328 387 265 1110 366 367 368 795 788 789 794 790 791 792 793 797 796 798 799 267 966 964 1094 1102 1103 1104 1105 1106 737 822 823 824 821 673 340 473 474 476 475 416 419 417 418 266 411 431 666 667 804 321 751 86 116 52 56 57 25 362 361 414 469 383 453 457 458 459 813 679 521 724 699 750 1115 382 752 188 627 185 636 647 783 341 371 407 420 421 422 924 316 477 423 648 603 131 132 133 134 136 137 139 140 141 144 147 142 135 143 138 146 145 122 605 519 518 530 942 816 438 436 439 440 441 801 805 71"
ext.run_qc = true
publishDir = [
path: { "${params.outdir}/${meta.id}/anat/"},
saveAs: {
filename ->
if ( filename.contains("CST_include_mask") ) { "${meta.id}_label-CST_desc-exclude_mask.nii.gz" }
else { params.lean_output ? null : filename }
}
]
}
withName: "CREATE_CST_INCLUDE" {
ext.suffix = "CST_include"
ext.labels_ids = "215 1205 1150 1158 1152 1151 1137 1265 1266 1155 115"
ext.run_qc = true
publishDir = [
path: { "${params.outdir}/${meta.id}/anat/"},
saveAs: {
filename ->
if ( filename.contains("CST_include_mask") ) { "${meta.id}_label-CST_desc-include_mask.nii.gz" }
else { params.lean_output ? null : filename }
}
]
}
withName: "CREATE_CST" {
ext.suffix = "CST"
ext.run_qc = true
publishDir = [
path: { "${params.outdir}/${meta.id}/dwi/"},
saveAs: {
filename ->
if ( filename.contains("CST_tracking.trk") ) { "${meta.id}_label-CST_desc-tracking.trk" }
else if ( filename.contains("CST_tracking_stats") ) { "${meta.id}_label-CST_desc-stats.json" }
else { params.lean_output ? null : filename }
}
]
}
withName: "CREATE_AC_EXCLUDE" {
ext.suffix = "AC_exclude"
ext.labels_ids = "470 512 724 801"
ext.run_qc = true
publishDir = [
path: { "${params.outdir}/${meta.id}/anat/"},
saveAs: {
filename ->
if ( filename.contains("AC_exclude_mask") ) { "${meta.id}_label-AC_desc-exclude_mask.nii.gz" }
else { params.lean_output ? null : filename }
}
]
}
withName: "CREATE_AC_INCLUDE" {
ext.suffix = "AC_include"
ext.labels_ids = "1119 1120"
ext.run_qc = true
publishDir = [
path: { "${params.outdir}/${meta.id}/anat/"},
saveAs: {
filename ->
if ( filename.contains("AC_include_mask") ) { "${meta.id}_label-AC_desc-include_mask.nii.gz" }
else { params.lean_output ? null : filename }
}
]
}
withName: "CREATE_CC_EXCLUDE" {
ext.suffix = "CC_exclude"
ext.labels_ids = "17 18 19 20 21 322 370 440 441 805 906 941 942 944 950 1119 1120 1127 1150 1152 1166 1205 1227 1319"
ext.run_qc = true
publishDir = [
path: { "${params.outdir}/${meta.id}/anat/"},
saveAs: {
filename ->
if ( filename.contains("CC_exclude_mask") ) { "${meta.id}_label-CC_desc-exclude_mask.nii.gz" }
else { params.lean_output ? null : filename }
}
]
}
withName: "CREATE_CC_INCLUDE" {
ext.suffix = "CC_include"
ext.labels_ids = "1139 1140 1141 1142 1173 1174 1179 1182"
ext.run_qc = true
publishDir = [
path: { "${params.outdir}/${meta.id}/anat/"},
saveAs: {
filename ->
if ( filename.contains("CC_include_mask") ) { "${meta.id}_label-CC_desc-include_mask.nii.gz" }
else { params.lean_output ? null : filename }
}
]
}
withName: "GETMIDSAGITTAL_CC" {
ext.suffix = "CC_midsagittal"
ext.run_qc = true
publishDir = [
path: { "${params.outdir}/${meta.id}/anat/"},
saveAs: {
filename ->
if ( filename.contains("CC_midsagittal_mask.nii.gz") ) { "${meta.id}_label-CC_desc-midsagittal_mask.nii.gz" }
else { params.lean_output ? null : filename }
}
]
}
withName: "GETMIDSAGITTAL_AC" {
ext.suffix = "AC_midsagittal"
ext.run_qc = true
publishDir = [
path: { "${params.outdir}/${meta.id}/anat/"},
saveAs: {
filename ->
if ( filename.contains("AC_midsagittal_mask.nii.gz") ) { "${meta.id}_label-AC_desc-midsagittal_mask.nii.gz" }
else { params.lean_output ? null : filename }
}
]
}
withName: "CREATE_CC" {
ext.suffix = "CC"
ext.run_qc = true
publishDir = [
path: { "${params.outdir}/${meta.id}/dwi/"},
saveAs: {
filename ->
if ( filename.contains("CC_tracking.trk") ) { "${meta.id}_label-CC_desc-tracking.trk" }
else if ( filename.contains("CC_tracking_stats") ) { "${meta.id}_label-CC_desc-stats.json" }
else { params.lean_output ? null : filename }
}
]
}
withName: "CREATE_AC" {
ext.suffix = "AC"
ext.run_qc = true
publishDir = [
path: { "${params.outdir}/${meta.id}/dwi/"},
saveAs: {
filename ->
if ( filename.contains("AC_tracking.trk") ) { "${meta.id}_label-AC_desc-tracking.trk" }
else if ( filename.contains("AC_tracking_stats") ) { "${meta.id}_label-AC_desc-stats.json" }
else { params.lean_output ? null : filename }
}
]
}
}
// Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile
// Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled
// Set to your registry if you have a mirror of containers
apptainer.registry = 'docker.io'
docker.registry = 'docker.io'
podman.registry = 'quay.io'
singularity.registry = 'docker.io'
charliecloud.registry = 'quay.io'
// Load igenomes.config if required
// includeConfig !params.igenomes_ignore ? 'conf/igenomes.config' : 'conf/igenomes_ignored.config'
// Export these variables to prevent local Python/R libraries from conflicting with those in the container
// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
env {
PYTHONNOUSERSITE = 1
R_PROFILE_USER = "/.Rprofile"
R_ENVIRON_USER = "/.Renviron"
JULIA_DEPOT_PATH = "/usr/local/share/julia"
}
// Disable process selector warnings by default. Use debug profile to enable warnings.
nextflow.enable.configProcessNamesValidation = false
timeline {
enabled = true
file = "${params.outdir}/pipeline_info/execution_timeline_${params.trace_report_suffix}.html"
}
report {
enabled = true
file = "${params.outdir}/pipeline_info/execution_report_${params.trace_report_suffix}.html"
}
trace {
enabled = true
file = "${params.outdir}/pipeline_info/execution_trace_${params.trace_report_suffix}.txt"
}
dag {
enabled = true
file = "${params.outdir}/pipeline_info/pipeline_dag_${params.trace_report_suffix}.html"
}
manifest {
name = 'scilus/sf-mouse'
contributors = [
[
name: 'Elise Cosenza',
affiliation: 'Université de Bordeaux',
email: '[email protected]',
github: '@EliseCos',
contribution: ['author'],
orcid: 'https://orcid.org/0009-0006-5294-1250' // List of contribution types ('author', 'maintainer' or 'contributor')
],
[
name: 'Arnaud Boré',
affiliation: 'Université de Sherbrooke',
email: '[email protected]',
github: '@arnaudbore',
contribution: ['author', 'maintainer'],
orcid: 'https://orcid.org/0000-0002-4822-1211'// List of contribution types ('author', 'maintainer' or 'contributor')
],
]
homePage = 'https://github.com/scilus/sf-mouse'
description = """sf-mouse is a neuroimaging pipeline to process ex-vivo dMRI data."""
mainScript = 'main.nf'
defaultBranch = 'master'
nextflowVersion = '!>=24.10.0'
version = ''
doi = ''
}
// Nextflow plugins
plugins {
id '[email protected]' // Validation of pipeline parameters and creation of an input channel from a sample sheet
}