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Merge pull request scilus#139 from arnaudbore/migrate_topup_eddy
Migrate Topup and Eddy modules to nf-test
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| name: "preproc_eddy" | ||
| channels: | ||
| - Docker | ||
| - Apptainer | ||
| dependencies: | ||
| - "FSL" | ||
| - "scilpy" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,61 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process PREPROC_EDDY" | ||
| script "../main.nf" | ||
| process "PREPROC_EDDY" | ||
|
|
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| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "preproc" | ||
| tag "preproc/eddy" | ||
|
|
||
| tag "subworkflows" | ||
| tag "subworkflows/load_test_data" | ||
|
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| config "./nextflow.config" | ||
|
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| setup { | ||
| run("LOAD_TEST_DATA", alias: "LOAD_DATA") { | ||
| script "../../../../../subworkflows/nf-scil/load_test_data/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = Channel.from( [ "topup_eddy_light.zip" ] ) | ||
| input[1] = "test.load-test-data" | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
|
||
| test("eddy") { | ||
| when { | ||
| process { | ||
| """ | ||
| input[0] = LOAD_DATA.out.test_data_directory | ||
| .map{ test_data_directory -> [ | ||
| [ id:'test', single_end:false ], // meta map | ||
| file("\${test_data_directory}/sub-01_dir-AP_dwi.nii.gz", checkIfExists: true), | ||
| file("\${test_data_directory}/sub-01_dir-AP_dwi.bval", checkIfExists: true), | ||
| file("\${test_data_directory}/sub-01_dir-AP_dwi.bvec", checkIfExists: true), | ||
| file("\${test_data_directory}/sub-01_dir-PA_dwi.nii.gz", checkIfExists: true), | ||
| file("\${test_data_directory}/sub-01_dir-PA_dwi.bval", checkIfExists: true), | ||
| file("\${test_data_directory}/sub-01_dir-PA_dwi.bvec", checkIfExists: true), | ||
| 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)]} | ||
| """ | ||
| } | ||
| } | ||
|
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||
| 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, | ||
| ).match() } | ||
| ) | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,31 @@ | ||
| { | ||
| "eddy": { | ||
| "content": [ | ||
| "test__dwi_corrected.nii.gz", | ||
| [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test__bval_eddy:md5,4c61c53078316c31b4d5daf446a3d6ac" | ||
| ] | ||
| ], | ||
| "test__dwi_eddy_corrected.bvec", | ||
| [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test__b0_bet_mask.nii.gz:md5,fc1f94e2a5e2cf5197d7fdc28a83ca28" | ||
| ] | ||
| ] | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "23.10.1" | ||
| }, | ||
| "timestamp": "2024-04-29T16:11:13.561798" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| preproc/eddy: | ||
| - "modules/nf-scil/preproc/eddy/**" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| name: "preproc_topup" | ||
| channels: | ||
| - Docker | ||
| - Apptainer | ||
| dependencies: | ||
| - "FSL" | ||
| - "scilpy" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,62 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process PREPROC_TOPUP" | ||
| script "../main.nf" | ||
| process "PREPROC_TOPUP" | ||
|
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| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "preproc" | ||
| tag "preproc/topup" | ||
|
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| tag "subworkflows" | ||
| tag "subworkflows/load_test_data" | ||
|
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| config "./nextflow.config" | ||
|
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| setup { | ||
| run("LOAD_TEST_DATA", alias: "LOAD_DATA") { | ||
| script "../../../../../subworkflows/nf-scil/load_test_data/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = Channel.from( [ "topup_eddy_light.zip" ] ) | ||
| input[1] = "test.load-test-data" | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
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||
| test("topup") { | ||
| when { | ||
| process { | ||
| """ | ||
| input[0] = LOAD_DATA.out.test_data_directory | ||
| .map{ test_data_directory -> [ | ||
| [ id:'test', single_end:false ], // meta map | ||
| file("\${test_data_directory}/sub-01_dir-AP_dwi.nii.gz", checkIfExists: true), | ||
| file("\${test_data_directory}/sub-01_dir-AP_dwi.bval", checkIfExists: true), | ||
| file("\${test_data_directory}/sub-01_dir-AP_dwi.bvec", checkIfExists: true), | ||
| file("\${test_data_directory}/sub-01_dir-AP_sbref.nii.gz", checkIfExists: true), | ||
| file("\${test_data_directory}/sub-01_dir-PA_dwi.nii.gz", checkIfExists: true), | ||
| file("\${test_data_directory}/sub-01_dir-PA_dwi.bval", checkIfExists: true), | ||
| file("\${test_data_directory}/sub-01_dir-PA_dwi.bvec", checkIfExists: true), | ||
| file("\${test_data_directory}/sub-01_dir-PA_sbref.nii.gz", checkIfExists: true)]} | ||
| input[1] = [] | ||
| """ | ||
| } | ||
| } | ||
|
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||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot( | ||
| file(process.out.topup_corrected_b0s.get(0).get(1)).name, | ||
| file(process.out.topup_fieldcoef.get(0).get(1)).name, | ||
| file(process.out.topup_movpart.get(0).get(1)).name, | ||
| file(process.out.rev_b0_warped.get(0).get(1)).name, | ||
| process.out.rev_b0_mean, | ||
| process.out.b0_mean).match() } | ||
| ) | ||
| } | ||
| } | ||
| } |
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