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same for anatomical_segmentation workflow
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@AlexVCaron
AlexVCaron committed Sep 5, 2024
1 parent faccae7 commit 0259258
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Showing 3 changed files with 56 additions and 56 deletions.
24 changes: 17 additions & 7 deletions subworkflows/nf-scil/anatomical_segmentation/tests/main.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,7 @@ nextflow_workflow {
script "../../load_test_data/main.nf"
process {
"""
input[0] = Channel.from( [ "heavy.zip" ] )
input[0] = Channel.from( [ "T1w.zip", "freesurfer_nifti.zip" ] )
input[1] = "test.load-test-data"
"""
}
Expand All @@ -32,10 +32,15 @@ nextflow_workflow {
when {
workflow {
"""
input[0] = LOAD_DATA.out.test_data_directory.map{
ch_split_test_data = LOAD_DATA.out.test_data_directory
.branch{
t1w: it.simpleName == "T1w"
freesurfer: it.simpleName == "freesurfer_nifti"
}
input[0] = ch_split_test_data.t1w.map{
test_data_directory -> [
[ id:'test', single_end:false ], // meta map
file("\${test_data_directory}/anat/anat_image.nii.gz", checkIfExists: true),
[ id:'test' ],
file("\${test_data_directory}/T1w.nii.gz", checkIfExists: true),
[]
]}
input[1] = []
Expand All @@ -56,12 +61,17 @@ nextflow_workflow {
when {
workflow {
"""
ch_split_test_data = LOAD_DATA.out.test_data_directory
.branch{
t1w: it.simpleName == "T1w"
freesurfer: it.simpleName == "freesurfer_nifti"
}
input[0] = []
input[1] = LOAD_DATA.out.test_data_directory.map{
input[1] = ch_split_test_data.freesurfer.map{
test_data_directory -> [
[ id:'test', single_end:false ], // meta map
file("\${test_data_directory}/freesurfer/aparc_aseg.nii.gz", checkIfExists: true),
file("\${test_data_directory}/freesurfer/wmparc.nii.gz", checkIfExists: true),
file("\${test_data_directory}/aparc+aseg.nii.gz", checkIfExists: true),
file("\${test_data_directory}/wmparc.nii.gz", checkIfExists: true),
[]
]}
"""
Expand Down
84 changes: 36 additions & 48 deletions subworkflows/nf-scil/anatomical_segmentation/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,7 @@
"id": "test",
"single_end": false
},
"test__mask_wm.nii.gz:md5,2dc635526adb6ef185300acc326ead13"
"test__mask_wm.nii.gz:md5,0ed4a06defc512b1b898d6e0c3ef678a"
]
],
"1": [
Expand All @@ -17,7 +17,7 @@
"id": "test",
"single_end": false
},
"test__mask_gm.nii.gz:md5,247106ed727133078fe262b0b8244071"
"test__mask_gm.nii.gz:md5,a363d6207419b08346a7c05c6525430e"
]
],
"2": [
Expand All @@ -26,7 +26,7 @@
"id": "test",
"single_end": false
},
"test__mask_csf.nii.gz:md5,b92db7e454c95afadea320a143912ce8"
"test__mask_csf.nii.gz:md5,3dbcb3eefb507bedab91fb80ed636f36"
]
],
"3": [
Expand All @@ -50,7 +50,7 @@
"id": "test",
"single_end": false
},
"test__mask_csf.nii.gz:md5,b92db7e454c95afadea320a143912ce8"
"test__mask_csf.nii.gz:md5,3dbcb3eefb507bedab91fb80ed636f36"
]
],
"gm_map": [
Expand All @@ -62,7 +62,7 @@
"id": "test",
"single_end": false
},
"test__mask_gm.nii.gz:md5,247106ed727133078fe262b0b8244071"
"test__mask_gm.nii.gz:md5,a363d6207419b08346a7c05c6525430e"
]
],
"versions": [
Expand All @@ -77,72 +77,66 @@
"id": "test",
"single_end": false
},
"test__mask_wm.nii.gz:md5,2dc635526adb6ef185300acc326ead13"
"test__mask_wm.nii.gz:md5,0ed4a06defc512b1b898d6e0c3ef678a"
]
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0-rc1",
"nextflow": "24.04.4"
},
"timestamp": "2024-05-09T20:53:29.945493"
"timestamp": "2024-09-05T02:45:52.364394"
},
"anatomical_segmentation - fslfast": {
"content": [
{
"0": [
[
{
"id": "test",
"single_end": false
"id": "test"
},
"test__mask_wm.nii.gz:md5,f849e268007a747714e342162f13f631"
"test__mask_wm.nii.gz:md5,98d75f5c0ddd2b7f2bfff8fbf1877e34"
]
],
"1": [
[
{
"id": "test",
"single_end": false
"id": "test"
},
"test__mask_gm.nii.gz:md5,39396421c6d1d32ea7943a5ec7a49dce"
"test__mask_gm.nii.gz:md5,a840f08c5b90cb351d3272d8cab6f00c"
]
],
"2": [
[
{
"id": "test",
"single_end": false
"id": "test"
},
"test__mask_csf.nii.gz:md5,d0fbc088059f17faff38fbcd33257d27"
"test__mask_csf.nii.gz:md5,f22037987a38e5132ccbb2887ee71842"
]
],
"3": [
[
{
"id": "test",
"single_end": false
"id": "test"
},
"test__map_wm.nii.gz:md5,1d5a9655d4e3c832b14c83e9424b00fc"
"test__map_wm.nii.gz:md5,c7d666c66baea2132d70be38017c6901"
]
],
"4": [
[
{
"id": "test",
"single_end": false
"id": "test"
},
"test__map_gm.nii.gz:md5,f7e51eb14af645c687db5d2c6a4f5bf4"
"test__map_gm.nii.gz:md5,6dbc993e43f6efcdd6a3a097df2b4574"
]
],
"5": [
[
{
"id": "test",
"single_end": false
"id": "test"
},
"test__map_csf.nii.gz:md5,9c14d8f70e69d641d9c214d0d52b3663"
"test__map_csf.nii.gz:md5,dcc224f10f31ee306491ebbdcfbe5bfe"
]
],
"6": [
Expand All @@ -151,37 +145,33 @@
"csf_map": [
[
{
"id": "test",
"single_end": false
"id": "test"
},
"test__map_csf.nii.gz:md5,9c14d8f70e69d641d9c214d0d52b3663"
"test__map_csf.nii.gz:md5,dcc224f10f31ee306491ebbdcfbe5bfe"
]
],
"csf_mask": [
[
{
"id": "test",
"single_end": false
"id": "test"
},
"test__mask_csf.nii.gz:md5,d0fbc088059f17faff38fbcd33257d27"
"test__mask_csf.nii.gz:md5,f22037987a38e5132ccbb2887ee71842"
]
],
"gm_map": [
[
{
"id": "test",
"single_end": false
"id": "test"
},
"test__map_gm.nii.gz:md5,f7e51eb14af645c687db5d2c6a4f5bf4"
"test__map_gm.nii.gz:md5,6dbc993e43f6efcdd6a3a097df2b4574"
]
],
"gm_mask": [
[
{
"id": "test",
"single_end": false
"id": "test"
},
"test__mask_gm.nii.gz:md5,39396421c6d1d32ea7943a5ec7a49dce"
"test__mask_gm.nii.gz:md5,a840f08c5b90cb351d3272d8cab6f00c"
]
],
"versions": [
Expand All @@ -190,27 +180,25 @@
"wm_map": [
[
{
"id": "test",
"single_end": false
"id": "test"
},
"test__map_wm.nii.gz:md5,1d5a9655d4e3c832b14c83e9424b00fc"
"test__map_wm.nii.gz:md5,c7d666c66baea2132d70be38017c6901"
]
],
"wm_mask": [
[
{
"id": "test",
"single_end": false
"id": "test"
},
"test__mask_wm.nii.gz:md5,f849e268007a747714e342162f13f631"
"test__mask_wm.nii.gz:md5,98d75f5c0ddd2b7f2bfff8fbf1877e34"
]
]
}
],
"meta": {
"nf-test": "0.8.4",
"nextflow": "23.10.1"
"nf-test": "0.9.0-rc1",
"nextflow": "24.04.4"
},
"timestamp": "2024-06-17T14:24:57.988893"
"timestamp": "2024-09-05T02:38:48.75146"
}
}
4 changes: 3 additions & 1 deletion tests/config/test_data.json
View file
Original file line number Diff line number Diff line change
Expand Up @@ -51,5 +51,7 @@
"T1w.zip": "8e9cf2beec4595d407732152a19589f5",
"dti.zip": "ba866c59fc4d984f626691a6b941fc32",
"responses.zip": "1a5b862b91c72740bcce0431a1f9254a",
"segmentation.zip": "ab51be6d142ad1a8e30ffb964447d010"
"segmentation.zip": "ab51be6d142ad1a8e30ffb964447d010",
"freesurfer_full.zip": "203e482426065326ff5920368d4d7908",
"freesurfer_nifti.zip": "adb5ac4cf5c45040339e04e7c142e8c9"
}

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