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Merged
arnaudbore merged 2 commits into from
Feb 27, 2026
Merged

Update registration, segmentation & betcrop #328

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6fcc334
Update containers for registration, seg and betcrop
levje Feb 27, 2026
e1bb71b
Merge branch 'main' into update-reg-seg-bet
levje Feb 27, 2026
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2 changes: 1 addition & 1 deletion modules/nf-neuro/betcrop/antsbet/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ process BETCROP_ANTSBET {
tag "$meta.id"
label 'process_high'

container 'scilus/scilus:2.2.0'
container 'scilus/scilus:2.2.2'

input:
tuple val(meta), path(t1), path(template), path(tissues_probabilities), path(mask), path(initial_affine)
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16 changes: 8 additions & 8 deletions modules/nf-neuro/betcrop/antsbet/tests/main.nf.test.snap
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Expand Up @@ -4,25 +4,25 @@
"test__t1_bet.nii.gz",
"test__t1_bet_mask.nii.gz",
[
"versions.yml:md5,25c425d0e08eacc9078fe72576a11b4e"
"versions.yml:md5,0f9b6797883796f1415a649503fa6035"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "25.04.7"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-10-09T19:38:39.066125477"
"timestamp": "2026-02-26T22:27:03.713538802"
},
"betcrop - antsbet - stub-run": {
"content": [
[
"versions.yml:md5,25c425d0e08eacc9078fe72576a11b4e"
"versions.yml:md5,0f9b6797883796f1415a649503fa6035"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "25.04.7"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-10-09T19:38:43.736867241"
"timestamp": "2026-02-26T22:27:08.31465089"
}
}
2 changes: 1 addition & 1 deletion modules/nf-neuro/betcrop/fslbetcrop/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ process BETCROP_FSLBETCROP {
tag "$meta.id"
label 'process_single'

container "scilus/scilus:2.2.0"
container "scilus/scilus:2.2.2"

input:
tuple val(meta), path(image), path(bval), path(bvec)
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38 changes: 19 additions & 19 deletions modules/nf-neuro/betcrop/fslbetcrop/tests/main.nf.test.snap
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Expand Up @@ -2,14 +2,14 @@
"betcrop - fslbetcrop - stub-run": {
"content": [
[
"versions.yml:md5,dc971e6f976ef949f2cf565392f3600e"
"versions.yml:md5,06b3bd7ed69358fbd2d2174309f145b7"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.7"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-30T13:29:28.969954"
"timestamp": "2026-02-26T22:28:09.239679593"
},
"betcrop - fslbetcrop - dwi": {
"content": [
Expand Down Expand Up @@ -42,7 +42,7 @@
]
],
"3": [
"versions.yml:md5,48fde397edb3c0c57fff98e427f1f579"
"versions.yml:md5,d98adbb6838a25ceadc22ff0229a7aee"
],
"bbox": [
[
Expand Down Expand Up @@ -72,15 +72,15 @@
]
],
"versions": [
"versions.yml:md5,48fde397edb3c0c57fff98e427f1f579"
"versions.yml:md5,d98adbb6838a25ceadc22ff0229a7aee"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.7"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-30T13:27:23.817381"
"timestamp": "2026-02-26T22:27:25.39706749"
},
"betcrop - fslbetcrop - t1": {
"content": [
Expand Down Expand Up @@ -113,7 +113,7 @@
]
],
"3": [
"versions.yml:md5,48fde397edb3c0c57fff98e427f1f579"
"versions.yml:md5,d98adbb6838a25ceadc22ff0229a7aee"
],
"bbox": [
[
Expand Down Expand Up @@ -143,15 +143,15 @@
]
],
"versions": [
"versions.yml:md5,48fde397edb3c0c57fff98e427f1f579"
"versions.yml:md5,d98adbb6838a25ceadc22ff0229a7aee"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.7"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-30T13:28:12.176385"
"timestamp": "2026-02-26T22:27:40.745798542"
},
"betcrop - fslbetcrop - t1 - dilate": {
"content": [
Expand Down Expand Up @@ -184,7 +184,7 @@
]
],
"3": [
"versions.yml:md5,48fde397edb3c0c57fff98e427f1f579"
"versions.yml:md5,d98adbb6838a25ceadc22ff0229a7aee"
],
"bbox": [
[
Expand Down Expand Up @@ -214,14 +214,14 @@
]
],
"versions": [
"versions.yml:md5,48fde397edb3c0c57fff98e427f1f579"
"versions.yml:md5,d98adbb6838a25ceadc22ff0229a7aee"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.7"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-30T13:29:00.369918"
"timestamp": "2026-02-26T22:27:58.046082616"
}
}
2 changes: 1 addition & 1 deletion modules/nf-neuro/registration/anattodwi/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ process REGISTRATION_ANATTODWI {
tag "$meta.id"
label 'process_single'

container "scilus/scilus:2.2.0"
container "scilus/scilus:2.2.2"

input:
tuple val(meta), path(fixed_reference), path(moving_anat), path(metric)
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12 changes: 6 additions & 6 deletions modules/nf-neuro/registration/anattodwi/tests/main.nf.test.snap
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Expand Up @@ -21,7 +21,7 @@
]
],
"10": [
"versions.yml:md5,f7db1ae1e2dd017daa92c91fbd41a28f"
"versions.yml:md5,37249bcc3b9ecbaf310960d876fd802d"
],
"2": [
[
Expand Down Expand Up @@ -210,26 +210,26 @@
]
],
"versions": [
"versions.yml:md5,f7db1ae1e2dd017daa92c91fbd41a28f"
"versions.yml:md5,37249bcc3b9ecbaf310960d876fd802d"
]
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-01-16T14:13:01.100817732"
"timestamp": "2026-02-26T22:29:56.358054216"
},
"registration - anattodwi -stub-run": {
"content": [
[
"versions.yml:md5,f7db1ae1e2dd017daa92c91fbd41a28f"
"versions.yml:md5,37249bcc3b9ecbaf310960d876fd802d"
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
"nextflow": "25.10.2"
},
"timestamp": "2025-10-28T12:57:40.842368795"
"timestamp": "2026-02-26T22:30:03.859914189"
}
}
2 changes: 1 addition & 1 deletion modules/nf-neuro/registration/ants/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ process REGISTRATION_ANTS {
tag "$meta.id"
label 'process_medium'

container "scilus/scilus:2.2.0"
container "scilus/scilus:2.2.2"

input:
tuple val(meta), path(fixed_image), path(moving_image), path(mask) //** optional, input = [] **//
Expand Down
24 changes: 12 additions & 12 deletions modules/nf-neuro/registration/ants/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,14 +2,14 @@
"registration - ants - stub": {
"content": [
[
"versions.yml:md5,78610891ed0adf1a5fe5f0de034d7555"
"versions.yml:md5,0b121e44c28b1c3efb04ae0dfc9ec76c"
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
"nextflow": "25.10.2"
},
"timestamp": "2025-10-28T13:00:52.757761907"
"timestamp": "2026-02-26T22:31:18.974318044"
},
"registration - ants - SyN quick": {
"content": [
Expand All @@ -31,7 +31,7 @@
]
],
"10": [
"versions.yml:md5,78610891ed0adf1a5fe5f0de034d7555"
"versions.yml:md5,0b121e44c28b1c3efb04ae0dfc9ec76c"
],
"2": [
[
Expand Down Expand Up @@ -202,15 +202,15 @@
]
],
"versions": [
"versions.yml:md5,78610891ed0adf1a5fe5f0de034d7555"
"versions.yml:md5,0b121e44c28b1c3efb04ae0dfc9ec76c"
]
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-01-16T14:58:50.566384471"
"timestamp": "2026-02-26T22:31:02.326829717"
},
"registration - ants - SyN": {
"content": [
Expand All @@ -232,7 +232,7 @@
]
],
"10": [
"versions.yml:md5,78610891ed0adf1a5fe5f0de034d7555"
"versions.yml:md5,0b121e44c28b1c3efb04ae0dfc9ec76c"
],
"2": [
[
Expand Down Expand Up @@ -393,15 +393,15 @@

],
"versions": [
"versions.yml:md5,78610891ed0adf1a5fe5f0de034d7555"
"versions.yml:md5,0b121e44c28b1c3efb04ae0dfc9ec76c"
]
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-01-16T14:58:18.910834696"
"timestamp": "2026-02-26T22:30:31.568063805"
},
"registration - ants - no warps": {
"content": [
Expand All @@ -423,7 +423,7 @@
]
],
"10": [
"versions.yml:md5,78610891ed0adf1a5fe5f0de034d7555"
"versions.yml:md5,0b121e44c28b1c3efb04ae0dfc9ec76c"
],
"2": [

Expand Down Expand Up @@ -556,14 +556,14 @@

],
"versions": [
"versions.yml:md5,78610891ed0adf1a5fe5f0de034d7555"
"versions.yml:md5,0b121e44c28b1c3efb04ae0dfc9ec76c"
]
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-01-16T14:58:57.816858804"
"timestamp": "2026-02-26T22:31:09.237312216"
}
}
2 changes: 1 addition & 1 deletion modules/nf-neuro/registration/antsapplytransforms/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ process REGISTRATION_ANTSAPPLYTRANSFORMS {
tag "$meta.id"
label 'process_low'

container "scilus/scilus:2.2.0"
container "scilus/scilus:2.2.2"

input:
tuple val(meta), path(images, arity: '1..*'), path(reference), path(transformations, arity: '1..*')
Expand Down
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