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[ENH] Get default data from subworkflow in meta.yml #306

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Merged
AlexVCaron merged 7 commits into from
Feb 16, 2026
Merged

[ENH] Get default data from subworkflow in meta.yml #306

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44f92f2
add subworkflow and test it with preproc_dwi
arnaudbore Feb 13, 2026
8c474ef
remove readme from claude
arnaudbore Feb 13, 2026
8c62e2e
fix linting - one warning remains
arnaudbore Feb 13, 2026
574874c
put synthstrip to false default
arnaudbore Feb 13, 2026
4119087
Merge branch 'main' into get_default_from_meta
arnaudbore Feb 13, 2026
01ba420
answer alex comments
arnaudbore Feb 16, 2026
ade0777
getOptionsWithDefaults takes object and we check type inside the func…
arnaudbore Feb 16, 2026
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5 changes: 3 additions & 2 deletions subworkflows/nf-neuro/preproc_dwi/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -15,6 +15,7 @@ include { IMAGE_RESAMPLE as RESAMPLE_DWI } from '../../../modules/nf-neuro/image
include { IMAGE_RESAMPLE as RESAMPLE_MASK } from '../../../modules/nf-neuro/image/resample/main'
include { UTILS_EXTRACTB0 } from '../../../modules/nf-neuro/utils/extractb0/main'
include { TOPUP_EDDY } from '../topup_eddy/main'
include { getOptionsWithDefaults } from '../utils_options/main'


workflow PREPROC_DWI {
Expand All @@ -30,8 +31,8 @@ workflow PREPROC_DWI {

main:

// Check to ensure options is a list of options,
assert options instanceof Map : "Options must be a Map, got ${options.getClass().getName()}"
// Merge options with defaults from meta.yml
options = getOptionsWithDefaults(options, "${moduleDir}/meta.yml")

ch_versions = channel.empty()
ch_multiqc_files = channel.empty()
Expand Down
13 changes: 12 additions & 1 deletion subworkflows/nf-neuro/preproc_dwi/meta.yml
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Expand Up @@ -90,6 +90,8 @@ components:
- utils/extractb0
- preproc/gibbs
- topup_eddy
- getoptionswithdefaults

input:
- ch_dwi:
type: file
Expand Down Expand Up @@ -147,7 +149,16 @@ input:
- preproc_dwi_run_normalize (bool): If 'true', the DWI will be normalized to have a mean value in the WM of approximately 1000 using MRtrix3's dwinormalise.
- preproc_dwi_run_resampling (bool): If 'true', the DWI will be resampled to 1 mm isotropic spatial resolution using DIPY's resample.
mandatory: true
default: {}
default:
preproc_dwi_run_denoising: true
preproc_dwi_run_degibbs: true
topup_eddy_run_topup: true
topup_eddy_run_eddy: true
preproc_dwi_run_synthstrip: false
preproc_dwi_keep_dwi_with_skull: false
preproc_dwi_run_N4: true
preproc_dwi_run_normalize: true
preproc_dwi_run_resampling: true
output:
- dwi_resample:
type: file
Expand Down
82 changes: 4 additions & 78 deletions subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test
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Expand Up @@ -22,6 +22,7 @@ nextflow_workflow {
tag "preproc/normalize"
tag "utils/extractb0"
tag "topup_eddy"
tag "subworkflows/utils_options"

tag "load_test_data"

Expand All @@ -41,7 +42,6 @@ nextflow_workflow {
}

test("preproc_dwi - AP DWI | skip steps") {
config "./nextflow_skipsteps.config"
when {
workflow {
"""
Expand All @@ -62,15 +62,12 @@ nextflow_workflow {
"topup_eddy_run_eddy": false,
"preproc_dwi_run_denoising": false,
"preproc_dwi_run_degibbs": false,
"preproc_dwi_run_N4": true,
"preproc_dwi_run_normalize": false,
"preproc_dwi_run_resampling": true,
"preproc_dwi_keep_dwi_with_skull": true
]
"""
}
}

then {
assertAll(
{ assert workflow.success },
Expand All @@ -92,7 +89,6 @@ nextflow_workflow {
}

test("preproc_dwi - AP DWI | PA sbref") {
config "./nextflow_synthstrip.config"
when {
workflow {
"""
Expand All @@ -113,20 +109,11 @@ nextflow_workflow {
input[4] = channel.empty()
input[5] = channel.from( [] )
input[6] = [
"topup_eddy_run_topup": true,
"topup_eddy_run_eddy": true,
"preproc_dwi_run_denoising": true,
"preproc_dwi_run_degibbs": true,
"preproc_dwi_run_N4": true,
"preproc_dwi_run_normalize": true,
"preproc_dwi_run_resampling": true,
"preproc_dwi_run_synthstrip": true,
"preproc_dwi_keep_dwi_with_skull": false
"preproc_dwi_run_synthstrip": true
]
"""
}
}

then {
assertAll(
{ assert workflow.success },
Expand All @@ -148,7 +135,6 @@ nextflow_workflow {
}

test("preproc_dwi - AP DWI | PA DWI") {
config "./nextflow_synthstrip.config"
when {
workflow {
"""
Expand All @@ -171,20 +157,11 @@ nextflow_workflow {
input[4] = channel.from("https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/requirements/synthstrip.1.pt")
input[5] = channel.from( [] )
input[6] = [
"topup_eddy_run_topup": true,
"topup_eddy_run_eddy": true,
"preproc_dwi_run_denoising": true,
"preproc_dwi_run_degibbs": true,
"preproc_dwi_run_N4": true,
"preproc_dwi_run_normalize": true,
"preproc_dwi_run_resampling": true,
"preproc_dwi_run_synthstrip": true,
"preproc_dwi_keep_dwi_with_skull": false
"preproc_dwi_run_synthstrip": true
]
"""
}
}

then {
assertAll(
{ assert workflow.success },
Expand All @@ -206,7 +183,6 @@ nextflow_workflow {
}

test("preproc_dwi - AP DWI+sbref | PA DWI+sbref") {
config "./nextflow_synthstrip.config"
when {
workflow {
"""
Expand Down Expand Up @@ -237,21 +213,10 @@ nextflow_workflow {
input[4] = channel.from("https://surfer.nmr.mgh.harvard.edu/docs/synthstrip/requirements/synthstrip.1.pt")
.map{ weights -> [ [ id:'test' ], weights ] }
input[5] = channel.from( [] )
input[6] = [
"topup_eddy_run_topup": true,
"topup_eddy_run_eddy": true,
"preproc_dwi_run_denoising": true,
"preproc_dwi_run_degibbs": true,
"preproc_dwi_run_N4": true,
"preproc_dwi_run_normalize": true,
"preproc_dwi_run_resampling": true,
"preproc_dwi_run_synthstrip": true,
"preproc_dwi_keep_dwi_with_skull": false
]
input[6] = [:]
"""
}
}

then {
assertAll(
{ assert workflow.success },
Expand All @@ -271,43 +236,4 @@ nextflow_workflow {
)
}
}

test("preproc_dwi - wrong options format - should fail") {
config "./nextflow_skipsteps.config"
when {
workflow {
"""
input[0] = LOAD_DATA.out.test_data_directory.map{
test_data_directory -> [
[ id:'test' ],
file("\${test_data_directory}/sub-01_dir-AP_dwi.nii.gz"),
file("\${test_data_directory}/sub-01_dir-AP_dwi.bval"),
file("\${test_data_directory}/sub-01_dir-AP_dwi.bvec")
]}
input[1] = channel.from( [] )
input[2] = channel.from( [] )
input[3] = channel.from( [] )
input[4] = channel.empty()
input[5] = channel.from( [] )
input[6] = channel.of([
"topup_eddy_run_topup": false,
"topup_eddy_run_eddy": false,
"preproc_dwi_run_denoising": false,
"preproc_dwi_run_degibbs": false,
"preproc_dwi_run_N4": true,
"preproc_dwi_run_normalize": false,
"preproc_dwi_run_resampling": true,
"preproc_dwi_keep_dwi_with_skull": true
])
"""
}
}

then {
assertAll(
{ assert workflow.failed },
{ assert workflow.stdout.contains("ERROR ~ Options must be a Map, got groovyx.gpars.dataflow.DataflowBroadcast. Expression: (options instanceof java.util.Map). Values: options = DataflowBroadcast around DataflowStream[?]") }
)
}
}
}
27 changes: 7 additions & 20 deletions subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -47,7 +47,7 @@
{
"id": "test"
},
"test_dwi_cropped_bbox.pkl"
"test__image_boundingBox.pkl"
]
],
"mqc": [
Expand Down Expand Up @@ -77,29 +77,16 @@
"test__rev_dwi_eddy_mqc.gif"
]
],
"pwd_avg": [
[
{
"id": "test"
},
"test_pwd_avg.nii.gz"
]
],
"versions": [
"versions.yml:md5,00c3e8560e74fb87cacb736eb5658fcb",
"versions.yml:md5,034b6d262d1e0e45c673d3ac1756e22f",
"versions.yml:md5,218c08543fae3d1e7dd9b1527aa67a21",
"versions.yml:md5,2b1e0ce850286655d4510ff462e0f57b",
"versions.yml:md5,3efc92963bc72284def5a9aeff469919",
"versions.yml:md5,4f645295735c7f79182fd589063e11a5",
"versions.yml:md5,6775dffbd2264e526ccdfde32db655b9",
"versions.yml:md5,73b36e0fa7fa782add714cca892bf09c",
"versions.yml:md5,76b89b06b38b2148b5af5d388d333763",
"versions.yml:md5,83bb1f168d146ca8d303c24584044f9f",
"versions.yml:md5,a585ae0f02b31e59f3f641836f5cb608",
"versions.yml:md5,c6674ec69abd660014fba145790ec070",
"versions.yml:md5,c7da6834a9868efe7d6878ae023a6782",
"versions.yml:md5,c9f89e6a31f3d2add46a0350e9ff799b",
"versions.yml:md5,d1da6ec93d46e17eff56d0e7f9dc085d",
"versions.yml:md5,dd4515fa7d32a40e94927fddf215ef18",
"versions.yml:md5,fcf20744f2d2ea2b1a57d549d53c8ee6"
]
Expand All @@ -109,7 +96,7 @@
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-02-05T22:18:20.502502877"
"timestamp": "2026-02-13T11:04:27.678692921"
},
"preproc_dwi - AP DWI | PA sbref": {
"content": [
Expand Down Expand Up @@ -217,9 +204,9 @@
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.8"
"nextflow": "25.10.2"
},
"timestamp": "2026-02-11T13:35:27.137234"
"timestamp": "2026-02-12T23:28:25.597720297"
},
"preproc_dwi - AP DWI | PA DWI": {
"content": [
Expand Down Expand Up @@ -331,7 +318,7 @@
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-02-05T22:16:59.844303539"
"timestamp": "2026-02-12T23:29:35.247048959"
},
"preproc_dwi - AP DWI | skip steps": {
"content": [
Expand Down Expand Up @@ -397,6 +384,6 @@
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-02-05T23:33:51.782441298"
"timestamp": "2026-02-13T10:59:51.74610525"
}
}
14 changes: 14 additions & 0 deletions subworkflows/nf-neuro/preproc_dwi/tests/nextflow.config
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Expand Up @@ -27,6 +27,20 @@ process {
ext.readout = 0.062
ext.extra_args = "--flm=linear --niter=2"
}
withName: "IMAGE_POWDERAVERAGE" {
ext.b0_thr = 10
}
withName: "CROPDWI" {
ext.output_bbox = true
ext.first_suffix = "dwi"
}
withName: "CROPMASK" {
ext.first_suffix = "mask"
}
withName: "CONVERT" {
ext.first_suffix = "mask"
ext.datatype = "uint8"
}
withName: "BETCROP_FSLBETCROP" {
ext.bet_f = 0.16
ext.b0_thr = 10
Expand Down
52 changes: 0 additions & 52 deletions subworkflows/nf-neuro/preproc_dwi/tests/nextflow_skipsteps.config
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