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fix _files in main.nf + update local tracking #35

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Merged
arnaudbore merged 3 commits into from
Jan 14, 2026
Merged

fix _files in main.nf + update local tracking #35

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670aa0f
fix _filesin main.nf + update local tracking
EliseCos Jan 13, 2026
b00d944
Merge branch 'main' into update_preqc
EliseCos Jan 13, 2026
e4ffb29
fix ch_dwi_bvalbvec
EliseCos Jan 14, 2026
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2 changes: 1 addition & 1 deletion main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -94,7 +94,7 @@ workflow {
}
else {
ch_after_preqc = ch_dwi_bvalbvec.dwi
bvs_after_preqc = ch_dwi_bvalbvec.bvs
bvs_after_preqc = ch_dwi_bvalbvec.bvs_files
}

if (params.run_denoising){
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2 changes: 1 addition & 1 deletion modules.json
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Expand Up @@ -58,7 +58,7 @@
},
"tracking/localtracking": {
"branch": "main",
"git_sha": "63dc80c43cdca798a5f11cd5124da35337a94ac5",
"git_sha": "ec4f04fd25e3167ba495094925027248722c1aad",
"installed_by": ["modules"]
},
"utils/extractb0": {
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15 changes: 11 additions & 4 deletions modules/nf-neuro/tracking/localtracking/main.nf
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Expand Up @@ -53,14 +53,21 @@ process TRACKING_LOCALTRACKING {
}

"""
# Set home directory. This is problematic if the container is run
# with non-root user which does not create a home directory. When
# running the local tracking using GPU, its trying to write to
# ~/.cache/ directory, causing the job to fail.
mkdir -p /tmp
export HOME=/tmp

export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
export OMP_NUM_THREADS=1
export OPENBLAS_NUM_THREADS=1

local_step="$local_step"
local_step_size="$local_step"
if [[ -z "$local_step" ]] && [[ -n "$local_step_pct" ]]; then
pixdim=\$(scil_header_print_info $wm --keys pixdim | tr -d '[]' | awk '{for(i=2;i<=4;i++) if(\$i>0 && (\$i<min || min=="")) min=\$i} END {print min}')
local_step=\$(awk -v pixdim="\$pixdim" -v pct="$local_step_pct" 'BEGIN {printf "--step %.6f", pixdim * pct / 100}')
local_step_size=\$(awk -v pixdim="\$pixdim" -v pct="$local_step_pct" 'BEGIN {printf "--step %.6f", pixdim * pct / 100}')
fi

if [ "${local_tracking_mask}" == "wm" ]; then
Expand Down Expand Up @@ -94,7 +101,7 @@ process TRACKING_LOCALTRACKING {
scil_tracking_local $fodf ${prefix}__local_seeding_mask.nii.gz \
${prefix}__local_tracking_mask.nii.gz tmp.trk $enable_gpu\
$local_algo $local_seeding $local_nbr_seeds\
$local_random_seed $local_step $local_theta\
$local_random_seed \$local_step_size $local_theta\
$local_sfthres $local_min_len\
$local_max_len $compress $basis -f

Expand All @@ -113,7 +120,7 @@ process TRACKING_LOCALTRACKING {
"random_seed": $task.ext.local_random_seed,
"is_compress": "${task.ext.local_compress_streamlines}",
"compress_value": $task.ext.local_compress_value,
"step": \${local_step/--step /},
"step": \${local_step_size/--step /},
"theta": $task.ext.local_theta,
"sfthres": $task.ext.local_sfthres,
"min_len": $task.ext.local_min_len,
Expand Down