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Merge pull request scilus#137 from gagnonanthony/denoising_2.0
Migrate denoising modules to scilpy 2.0.0 + nf-test.
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,9 @@ | ||
| name: denoising_mppca | ||
|
|
||
| channels: | ||
| - Docker | ||
| - Apptainer | ||
|
|
||
| dependencies: | ||
| - FSL | ||
| - Mrtrix |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,52 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process DENOISING_MPPCA" | ||
| script "../main.nf" | ||
| process "DENOISING_MPPCA" | ||
| config "./nextflow.config" | ||
|
|
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| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "denoising" | ||
| tag "denoising/mppca" | ||
|
|
||
| tag "subworkflows" | ||
| tag "subworkflows/load_test_data" | ||
|
|
||
| test("denoising - mppca") { | ||
|
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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( [ "heavy.zip" ] ) | ||
| input[1] = "test.load-test-data" | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
|
||
| 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}/dwi/dwi.nii.gz") | ||
| ] | ||
| } | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,37 @@ | ||
| { | ||
| "denoising - mppca": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test_dwi_denoised.nii.gz:md5,c949b91d96513cba506975c271e53596" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,fb589ae27eb3edb1cd1a50b0e13d2714" | ||
| ], | ||
| "image": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test_dwi_denoised.nii.gz:md5,c949b91d96513cba506975c271e53596" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,fb589ae27eb3edb1cd1a50b0e13d2714" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "23.10.1" | ||
| }, | ||
| "timestamp": "2024-04-25T11:07:06.152814" | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,6 @@ | ||
| process { | ||
| withNAME: "DENOISING_MPPCA" { | ||
| publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } | ||
| ext.extent = 3 | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| denoising/mppca: | ||
| - "modules/nf-scil/denoising/mppca/**" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| --- | ||
| name: "denoising_nlmeans" | ||
| channels: | ||
| - Docker | ||
| - Apptainer | ||
| dependencies: | ||
| - "Scilpy" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,78 @@ | ||
| nextflow_process { | ||
|
|
||
| name "Test Process DENOISING_NLMEANS" | ||
| script "../main.nf" | ||
| process "DENOISING_NLMEANS" | ||
| config "./nextflow.config" | ||
|
|
||
| tag "modules" | ||
| tag "modules_nfcore" | ||
| tag "denoising" | ||
| tag "denoising/nlmeans" | ||
|
|
||
| tag "subworkflows" | ||
| tag "subworkflows/load_test_data" | ||
|
|
||
| setup { | ||
| run("LOAD_TEST_DATA", alias: "LOAD_DATA") { | ||
| script "../../../../../subworkflows/nf-scil/load_test_data/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = Channel.from( [ "heavy.zip" ] ) | ||
| input[1] = "test.load-test-data" | ||
| """ | ||
| } | ||
| } | ||
| } | ||
|
|
||
| test("denoising - nlmeans") { | ||
|
|
||
| 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}/anat/anat_image.nii.gz"), | ||
| [] | ||
| ] | ||
| } | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
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| test("denoising - nlmeans - withmask") { | ||
|
|
||
| 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}/anat/anat_image.nii.gz"), | ||
| file("\${test_data_directory}/anat/anat_mask.nii.gz") | ||
| ] | ||
| } | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,72 @@ | ||
| { | ||
| "denoising - nlmeans": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test_denoised.nii.gz:md5,4a4eaa8956682b97589682c62c3226e5" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,e5c9936e9d01b8503f706aecd0a39027" | ||
| ], | ||
| "image": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test_denoised.nii.gz:md5,4a4eaa8956682b97589682c62c3226e5" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,e5c9936e9d01b8503f706aecd0a39027" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "23.10.1" | ||
| }, | ||
| "timestamp": "2024-04-23T21:07:32.369936" | ||
| }, | ||
| "denoising - nlmeans - withmask": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test_denoised.nii.gz:md5,a4925934f71fc40c2182e8c1d3bc6687" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| "versions.yml:md5,e5c9936e9d01b8503f706aecd0a39027" | ||
| ], | ||
| "image": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false | ||
| }, | ||
| "test_denoised.nii.gz:md5,a4925934f71fc40c2182e8c1d3bc6687" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,e5c9936e9d01b8503f706aecd0a39027" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.8.4", | ||
| "nextflow": "23.10.1" | ||
| }, | ||
| "timestamp": "2024-04-23T21:09:03.715606" | ||
| } | ||
| } |
2 changes: 0 additions & 2 deletions
2
...nf-scil/denoising/nlmeans/nextflow.config → ...l/denoising/nlmeans/tests/nextflow.config
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,5 +1,3 @@ | ||
| process { | ||
|
|
||
| publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } | ||
|
|
||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,2 @@ | ||
| denoising/nlmeans: | ||
| - "modules/nf-scil/denoising/nlmeans/**" |
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