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[ENH] Update preproc modules #31

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[ENH] Update preproc modules #31

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8ff0ada
update preproc module
ThoumyreStanislas Oct 30, 2024
6704412
add test eddy full
ThoumyreStanislas Oct 31, 2024
633bb92
Merge branch 'main' of github.com:scilus/nf-neuro into port_module_pr…
ThoumyreStanislas Oct 31, 2024
a033541
fix test eddy
ThoumyreStanislas Oct 31, 2024
42dfd60
Merge branch 'main' of github.com:scilus/nf-neuro into port_module_pr…
ThoumyreStanislas Oct 31, 2024
48ff940
Merge branch 'main' of github.com:scilus/nf-neuro into port_module_pr…
ThoumyreStanislas Nov 1, 2024
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20 changes: 10 additions & 10 deletions modules/nf-neuro/preproc/eddy/main.nf
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Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
process PREPROC_EDDY {
tag "$meta.id"
label 'process_single'
label 'process_high'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
"https://scil.usherbrooke.ca/containers/scilus_2.0.0.sif":
"scilus/scilus:2.0.0"}"
"https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif":
"scilus/scilus:2.0.2"}"

input:
tuple val(meta), path(dwi), path(bval), path(bvec), path(rev_dwi), path(rev_bval), path(rev_bvec), path(corrected_b0s), path(topup_fieldcoef), path(topup_movpart)
Expand Down Expand Up @@ -34,8 +34,8 @@ process PREPROC_EDDY {
def extra_args = task.ext.extra_args ?: ""

"""
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
export OMP_NUM_THREADS=1
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=$task.cpus
export OMP_NUM_THREADS=$task.cpus
export OPENBLAS_NUM_THREADS=1
export ANTS_RANDOM_SEED=7468

Expand All @@ -62,7 +62,7 @@ process PREPROC_EDDY {
# If topup has been run before
if [[ -f "$topup_fieldcoef" ]]
then
mrconvert $corrected_b0s b0_corrected.nii.gz -coord 3 0 -axes 0,1,2 -nthreads 1
mrconvert $corrected_b0s b0_corrected.nii.gz -coord 3 0 -axes 0,1,2 -nthreads $task.cpus
bet b0_corrected.nii.gz ${prefix}__b0_bet.nii.gz -m -R\
-f $bet_topup_before_eddy_f

Expand All @@ -80,7 +80,7 @@ process PREPROC_EDDY {
bet ${prefix}__b0.nii.gz ${prefix}__b0_bet.nii.gz -m -R -f $bet_prelim_f
scil_volume_math.py convert ${prefix}__b0_bet_mask.nii.gz ${prefix}__b0_bet_mask.nii.gz --data_type uint8 -f
maskfilter ${prefix}__b0_bet_mask.nii.gz dilate ${prefix}__b0_bet_mask_dilated.nii.gz\
--npass $dilate_b0_mask_prelim_brain_extraction -nthreads 1
--npass $dilate_b0_mask_prelim_brain_extraction -nthreads $task.cpus
scil_volume_math.py multiplication ${prefix}__b0.nii.gz ${prefix}__b0_bet_mask_dilated.nii.gz\
${prefix}__b0_bet.nii.gz --data_type float32 -f

Expand All @@ -93,7 +93,7 @@ process PREPROC_EDDY {

echo "--very_verbose $extra_args" >> eddy.sh
sh eddy.sh
scil_volume_math.py lower_threshold dwi_eddy_corrected.nii.gz 0 ${prefix}__dwi_corrected.nii.gz
scil_volume_math.py lower_clip dwi_eddy_corrected.nii.gz 0 ${prefix}__dwi_corrected.nii.gz

if [[ \$number_rev_dwi -eq 0 ]]
then
Expand All @@ -106,7 +106,7 @@ process PREPROC_EDDY {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: 2.0.0
scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
mrtrix: \$(dwidenoise -version 2>&1 | sed -n 's/== dwidenoise \\([0-9.]\\+\\).*/\\1/p')
fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')
END_VERSIONS
Expand Down Expand Up @@ -135,7 +135,7 @@ process PREPROC_EDDY {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: 2.0.0
scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
mrtrix: \$(dwidenoise -version 2>&1 | sed -n 's/== dwidenoise \\([0-9.]\\+\\).*/\\1/p')
fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')

Expand Down
64 changes: 59 additions & 5 deletions modules/nf-neuro/preproc/eddy/tests/main.nf.test
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Expand Up @@ -19,18 +19,73 @@ nextflow_process {
script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
process {
"""
input[0] = Channel.from( [ "topup_eddy_light.zip" ] )
input[0] = Channel.from( [ "raw_DWIss1000-dir32.zip", "TOPUP.zip", "topup_eddy_light.zip" ] )
input[1] = "test.load-test-data"
"""
}
}
}

test("eddy") {
test("eddy_light") {

config "./nextflow.config"

when {
process {
"""
input[0] = LOAD_DATA.out.test_data_directory
ch_split_test_data = LOAD_DATA.out.test_data_directory
.branch{
raw_dwi: it.simpleName == "raw_DWIss1000-dir32"
topup_results: it.SimpleName == "TOPUP"
rev_dwi: it.simpleName == "topup_eddy_light"
}
ch_raw_dwi = ch_split_test_data.raw_dwi
.map{ test_data_directory -> [
[ id:'test', single_end:false ], // meta map
file("\${test_data_directory}/dwi.nii.gz", checkIfExists: true),
file("\${test_data_directory}/dwi.bval", checkIfExists: true),
file("\${test_data_directory}/dwi.bvec", checkIfExists: true),
[],
[],
[]]}
ch_topup = ch_split_test_data.topup_results
.map{ test_data_directory -> [
[ id:'test', single_end:false ], // meta map
file("\${test_data_directory}/topup_corrected_b0s.nii.gz", checkIfExists: true),
file("\${test_data_directory}/topup_fieldcoef.nii.gz", checkIfExists: true),
file("\${test_data_directory}/topup_movpar.txt", checkIfExists: true)]}
input[0] = ch_raw_dwi.join(ch_topup)
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(
file(process.out.dwi_corrected.get(0).get(1)).name,
process.out.bval_corrected,
file(process.out.bvec_corrected.get(0).get(1)).name,
process.out.b0_mask,
process.out.versions
).match() }
)
}
}

test("eddy_full") {

config "./nextflow_full.config"

when {
process {
"""
ch_split_test_data = LOAD_DATA.out.test_data_directory
.branch{
raw_dwi: it.simpleName == "raw_DWIss1000-dir32"
topup_results: it.SimpleName == "TOPUP"
rev_dwi: it.simpleName == "topup_eddy_light"
}
input[0] = ch_split_test_data.rev_dwi
.map{ test_data_directory -> [
[ id:'test', single_end:false ], // meta map
file("\${test_data_directory}/sub-01_dir-AP_dwi.nii.gz", checkIfExists: true),
Expand All @@ -42,10 +97,9 @@ nextflow_process {
file("\${test_data_directory}/sub-01__corrected_b0s.nii.gz", checkIfExists: true),
file("\${test_data_directory}/topup_results_fieldcoef.nii.gz", checkIfExists: true),
file("\${test_data_directory}/topup_results_movpar.txt", checkIfExists: true)]}
"""
"""
}
}

then {
assertAll(
{ assert process.success },
Expand Down
44 changes: 38 additions & 6 deletions modules/nf-neuro/preproc/eddy/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{
"eddy": {
"eddy_full": {
"content": [
"test__dwi_corrected.nii.gz",
[
Expand All @@ -18,17 +18,49 @@
"id": "test",
"single_end": false
},
"test__b0_bet_mask.nii.gz:md5,fc1f94e2a5e2cf5197d7fdc28a83ca28"
"test__b0_bet_mask.nii.gz:md5,a1e4b4842cbdf57ab34d6803e64f8383"
]
],
[
"versions.yml:md5,2162950d257422ffda17cc7ac676c81d"
"versions.yml:md5,137e3ce0fd25e5b16de2d8cc5a5aefca"
]
],
"meta": {
"nf-test": "0.9.0-rc1",
"nextflow": "24.04.2"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-07-22T03:27:48.011429"
"timestamp": "2024-10-31T18:53:32.412097643"
},
"eddy_light": {
"content": [
"test__dwi_corrected.nii.gz",
[
[
{
"id": "test",
"single_end": false
},
"test__bval_eddy:md5,7995daabbd74fcf7c365a39a779f67e9"
]
],
"test__dwi_eddy_corrected.bvec",
[
[
{
"id": "test",
"single_end": false
},
"test__b0_bet_mask.nii.gz:md5,2dd16e0c664c910f1970b96056866fea"
]
],
[
"versions.yml:md5,137e3ce0fd25e5b16de2d8cc5a5aefca"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-10-31T13:17:58.524376706"
}
}
2 changes: 1 addition & 1 deletion modules/nf-neuro/preproc/eddy/tests/nextflow.config
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
process {
withName: "PREPROC_EDDY" {
ext.prefix_topup = "topup_results"
ext.prefix_topup = "topup"
ext.default_config_topup = "b02b0.cnf"
ext.encoding = "y"
ext.readout = 0.062
Expand Down
15 changes: 15 additions & 0 deletions modules/nf-neuro/preproc/eddy/tests/nextflow_full.config
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@@ -0,0 +1,15 @@
process {
withName: "PREPROC_EDDY" {
ext.prefix_topup = "topup_results"
ext.default_config_topup = "b02b0.cnf"
ext.encoding = "y"
ext.readout = 0.062
ext.b0_thr_extract_b0 = 10
ext.slice_drop_flag = true
ext.bet_topup_before_eddy_f=0.16
ext.eddy_cmd="eddy_cpu"
ext.dilate_b0_mask_prelim_brain_extraction = 5
ext.bet_prelim_f = 0.16
ext.extra_args = "--flm=linear --niter=2"
}
}
7 changes: 4 additions & 3 deletions modules/nf-neuro/preproc/n4/main.nf
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
process PREPROC_N4 {
tag "$meta.id"
label 'process_single'
label 'process_medium'
label "process_high_memory"

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
Expand Down Expand Up @@ -49,7 +50,7 @@ process PREPROC_N4 {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: 2.0.2
scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
N4BiasFieldCorrection: \$(N4BiasFieldCorrection --version 2>&1 | sed -n 's/ANTs Version: v\\([0-9.]\\+\\)/\\1/p')
END_VERSIONS
"""
Expand All @@ -65,7 +66,7 @@ process PREPROC_N4 {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: 2.0.2
scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
N4BiasFieldCorrection: \$(N4BiasFieldCorrection --version 2>&1 | sed -n 's/ANTs Version: v\\([0-9.]\\+\\)/\\1/p')
END_VERSIONS
"""
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-neuro/preproc/n4/meta.yml
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Expand Up @@ -7,7 +7,7 @@ keywords:
- N4
- bias field
tools:
- "Scilpy":
- "scilpy":
description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
homepage: "https://github.com/scilus/scilpy.git"

Expand Down
12 changes: 6 additions & 6 deletions modules/nf-neuro/preproc/n4/tests/main.nf.test.snap
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Expand Up @@ -29,10 +29,10 @@
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-10T16:06:45.886061"
"timestamp": "2024-10-30T13:19:29.130623074"
},
"preproc - n4 - anat": {
"content": [
Expand Down Expand Up @@ -64,9 +64,9 @@
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-10T16:09:11.896134"
"timestamp": "2024-10-30T13:23:00.282856"
}
}
4 changes: 2 additions & 2 deletions modules/nf-neuro/preproc/normalize/main.nf
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Expand Up @@ -43,7 +43,7 @@ process PREPROC_NORMALIZE {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: 2.0.2
scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
mrtrix: \$(dwidenoise -version 2>&1 | sed -n 's/== dwidenoise \\([0-9.]\\+\\).*/\\1/p')
END_VERSIONS
"""
Expand All @@ -63,7 +63,7 @@ process PREPROC_NORMALIZE {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: 2.0.2
scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
mrtrix: \$(dwidenoise -version 2>&1 | sed -n 's/== dwidenoise \\([0-9.]\\+\\).*/\\1/p')
END_VERSIONS
"""
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-neuro/preproc/normalize/meta.yml
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Expand Up @@ -8,7 +8,7 @@ keywords:
- scilpy
- MRtrix3
tools:
- "Scilpy":
- "scilpy":
description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
homepage: "https://github.com/scilus/scilpy.git"
- "MRtrix3":
Expand Down
10 changes: 5 additions & 5 deletions modules/nf-neuro/preproc/topup/main.nf
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Expand Up @@ -3,12 +3,12 @@ process PREPROC_TOPUP {
label 'process_single'

container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
"https://scil.usherbrooke.ca/containers/scilus_2.0.0.sif":
"scilus/scilus:2.0.0"}"
"https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif":
"scilus/scilus:2.0.2"}"

input:
tuple val(meta), path(dwi), path(bval), path(bvec), path(b0), path(rev_dwi), path(rev_bval), path(rev_bvec), path(rev_b0)
path(config_topup)
val(config_topup)

output:
tuple val(meta), path("*__corrected_b0s.nii.gz"), emit: topup_corrected_b0s
Expand Down Expand Up @@ -65,7 +65,7 @@ process PREPROC_TOPUP {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: 2.0.0
scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
antsRegistration: 2.4.3
fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')

Expand All @@ -91,7 +91,7 @@ process PREPROC_TOPUP {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
scilpy: 2.0.0
scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
antsRegistration: 2.4.3
fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')

Expand Down
2 changes: 1 addition & 1 deletion modules/nf-neuro/preproc/topup/meta.yml
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Expand Up @@ -10,7 +10,7 @@ tools:
- "FSL":
description: "FSL Toolbox and Scilpy Toolbox"
homepage: "https://fsl.fmrib.ox.ac.uk/fsl/fslwiki"
- "Scilpy":
- "scilpy":
description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
homepage: "https://github.com/scilus/scilpy.git"

Expand Down
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