diff --git a/modules/nf-scil/reconst/dtimetrics/main.nf b/modules/nf-scil/reconst/dtimetrics/main.nf index 159f0b1e..1a19d217 100644 --- a/modules/nf-scil/reconst/dtimetrics/main.nf +++ b/modules/nf-scil/reconst/dtimetrics/main.nf @@ -64,7 +64,7 @@ process RECONST_DTIMETRICS { if ( task.ext.rd ) args += " --rd ${prefix}__rd.nii.gz" if ( task.ext.tensor ) args += " --tensor ${prefix}__tensor.nii.gz" if ( task.ext.nonphysical ) args += " --non-physical ${prefix}__nonphysical.nii.gz" - if ( task.ext.pulsation ) args += " --pulsation ${prefix}__pulsation_std_dwi.nii.gz" + if ( task.ext.pulsation ) args += " --pulsation ${prefix}__pulsation.nii.gz" if ( task.ext.residual ) args += " --residual ${prefix}__residual.nii.gz" diff --git a/modules/nf-scil/reconst/dtimetrics/tests/main.nf.test b/modules/nf-scil/reconst/dtimetrics/tests/main.nf.test index b5c89272..89aa1e9c 100644 --- a/modules/nf-scil/reconst/dtimetrics/tests/main.nf.test +++ b/modules/nf-scil/reconst/dtimetrics/tests/main.nf.test @@ -46,7 +46,35 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + niftiMD5SUM(process.out.ad.get(0).get(1), 6), + niftiMD5SUM(process.out.evecs.get(0).get(1), 6), + niftiMD5SUM(process.out.evecs_v1.get(0).get(1), 6), + niftiMD5SUM(process.out.evecs_v2.get(0).get(1), 6), + niftiMD5SUM(process.out.evecs_v3.get(0).get(1), 6), + niftiMD5SUM(process.out.evals.get(0).get(1), 6), + niftiMD5SUM(process.out.evals_e1.get(0).get(1), 6), + niftiMD5SUM(process.out.evals_e2.get(0).get(1), 6), + niftiMD5SUM(process.out.evals_e3.get(0).get(1), 6), + niftiMD5SUM(process.out.fa.get(0).get(1), 6), + niftiMD5SUM(process.out.ga.get(0).get(1), 6), + niftiMD5SUM(process.out.rgb.get(0).get(1), 6), + niftiMD5SUM(process.out.md.get(0).get(1), 6), + niftiMD5SUM(process.out.mode.get(0).get(1), 6), + niftiMD5SUM(process.out.norm.get(0).get(1), 6), + niftiMD5SUM(process.out.rd.get(0).get(1), 6), + niftiMD5SUM(process.out.tensor.get(0).get(1), 6), + niftiMD5SUM(process.out.nonphysical.get(0).get(1), 6), + niftiMD5SUM(process.out.pulsation_std_dwi.get(0).get(1), 6), + niftiMD5SUM(process.out.residual.get(0).get(1), 6), + process.out.residual_iqr_residuals, + process.out.residual_mean_residuals, + process.out.residual_q1_residuals, + process.out.residual_q3_residuals, + process.out.residual_residuals_stats, + process.out.residual_std_residuals, + process.out.versions + ).match() } ) } @@ -75,9 +103,11 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + niftiMD5SUM(process.out.fa.get(0).get(1), 6), + process.out.versions + ).match() } ) } - } } diff --git a/modules/nf-scil/reconst/dtimetrics/tests/main.nf.test.snap b/modules/nf-scil/reconst/dtimetrics/tests/main.nf.test.snap index 1f2ce555..f85407b9 100644 --- a/modules/nf-scil/reconst/dtimetrics/tests/main.nf.test.snap +++ b/modules/nf-scil/reconst/dtimetrics/tests/main.nf.test.snap @@ -1,660 +1,101 @@ { "reconst - dtimetrics_with_b0mask": { "content": [ - { - "0": [ - - ], - "1": [ - - ], - "10": [ - - ], - "11": [ - - ], - "12": [ - - ], - "13": [ - - ], - "14": [ - - ], - "15": [ - - ], - "16": [ - - ], - "17": [ - - ], - "18": [ - - ], - "19": [ - - ], - "2": [ - - ], - "20": [ - - ], - "21": [ - - ], - "22": [ - - ], - "23": [ - - ], - "24": [ - - ], - "25": [ - - ], - "26": [ - "versions.yml:md5,f057a83131297624fb6d9db93df8d749" - ], - "3": [ - - ], - "4": [ - - ], - "5": [ - - ], - "6": [ - - ], - "7": [ - - ], - "8": [ - - ], - "9": [ - [ - { - "id": "test", - "single_end": false - }, - "test__fa.nii.gz:md5,2faf9f0eb4fa3617611ffb26467dad46" - ] - ], - "ad": [ - - ], - "evals": [ - - ], - "evals_e1": [ - - ], - "evals_e2": [ - - ], - "evals_e3": [ - - ], - "evecs": [ - - ], - "evecs_v1": [ - - ], - "evecs_v2": [ - - ], - "evecs_v3": [ - - ], - "fa": [ - [ - { - "id": "test", - "single_end": false - }, - "test__fa.nii.gz:md5,2faf9f0eb4fa3617611ffb26467dad46" - ] - ], - "ga": [ - - ], - "md": [ - - ], - "mode": [ - - ], - "nonphysical": [ - - ], - "norm": [ - - ], - "pulsation_std_dwi": [ - - ], - "rd": [ - - ], - "residual": [ - - ], - "residual_iqr_residuals": [ - - ], - "residual_mean_residuals": [ - - ], - "residual_q1_residuals": [ - - ], - "residual_q3_residuals": [ - - ], - "residual_residuals_stats": [ - - ], - "residual_std_residuals": [ - - ], - "rgb": [ - - ], - "tensor": [ - - ], - "versions": [ - "versions.yml:md5,f057a83131297624fb6d9db93df8d749" - ] - } + "test__fa.nii.gz:md5,4da8c2e248c0d93a018d0add9bbc6438", + [ + "versions.yml:md5,f057a83131297624fb6d9db93df8d749" + ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0-rc1", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-07T15:06:18.845384" + "timestamp": "2024-08-26T14:44:59.223632" }, "reconst - dtimetrics": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test__ad.nii.gz:md5,ece4e1d0fc03f4bafc882b63285984d3" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test__evecs.nii.gz:md5,12a42297c1c257336f1b5cb04cd18a45" - ] - ], - "10": [ - [ - { - "id": "test", - "single_end": false - }, - "test__ga.nii.gz:md5,209ab956ff7e59217db0929c5dff08fa" - ] - ], - "11": [ - [ - { - "id": "test", - "single_end": false - }, - "test__rgb.nii.gz:md5,601b67930e79dbf23dfaeb5aafe6f3e7" - ] - ], - "12": [ - [ - { - "id": "test", - "single_end": false - }, - "test__md.nii.gz:md5,d9a6ca6d7ad205b8ec0a90f0db4c53d9" - ] - ], - "13": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mode.nii.gz:md5,015a1e5541e9fbb720e1c4110ebbcc46" - ] - ], - "14": [ - [ - { - "id": "test", - "single_end": false - }, - "test__norm.nii.gz:md5,9b90f4e4af148a4d0395596fb48b5bef" - ] - ], - "15": [ - [ - { - "id": "test", - "single_end": false - }, - "test__rd.nii.gz:md5,d33a7089844a53184c0548cdf8899efa" - ] - ], - "16": [ - [ - { - "id": "test", - "single_end": false - }, - "test__tensor.nii.gz:md5,9eac2b7afe5db2d65650f1307e3b8166" - ] - ], - "17": [ - [ - { - "id": "test", - "single_end": false - }, - "test__nonphysical.nii.gz:md5,7da6de5ad6e7c37518f9f3962f066f89" - ] - ], - "18": [ - - ], - "19": [ - [ - { - "id": "test", - "single_end": false - }, - "test__residual.nii.gz:md5,4d91b617b09018cdc3feb07256665d1b" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test__evecs_v1.nii.gz:md5,b9b02ffa0ba41ec5e9e52f18c7741f18" - ] - ], - "20": [ - [ - { - "id": "test", - "single_end": false - }, - "test__residual_iqr_residuals.npy:md5,4a71d46303bb3ac67088fe5cdaa5694a" - ] - ], - "21": [ - [ - { - "id": "test", - "single_end": false - }, - "test__residual_mean_residuals.npy:md5,2247858eaf51c6e973649418f8721477" - ] - ], - "22": [ - [ - { - "id": "test", - "single_end": false - }, - "test__residual_q1_residuals.npy:md5,4a71d46303bb3ac67088fe5cdaa5694a" - ] - ], - "23": [ - [ - { - "id": "test", - "single_end": false - }, - "test__residual_q3_residuals.npy:md5,4a71d46303bb3ac67088fe5cdaa5694a" - ] - ], - "24": [ - [ - { - "id": "test", - "single_end": false - }, - "test__residual_residuals_stats.png:md5,18ce14e9e554c8f5fb1cf0c87af36f9f" - ] - ], - "25": [ - [ - { - "id": "test", - "single_end": false - }, - "test__residual_std_residuals.npy:md5,5e526c12b8a13b611bd1b2e00d4e1448" - ] - ], - "26": [ - "versions.yml:md5,f057a83131297624fb6d9db93df8d749" - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test__evecs_v2.nii.gz:md5,2189cde6872fb140683a1cd6c5eb1e9e" - ] - ], - "4": [ - [ - { - "id": "test", - "single_end": false - }, - "test__evecs_v3.nii.gz:md5,af227812521827a9064e3a8596fffcda" - ] - ], - "5": [ - [ - { - "id": "test", - "single_end": false - }, - "test__evals.nii.gz:md5,464d861a0ddda845824b8a4c778d1b6b" - ] - ], - "6": [ - [ - { - "id": "test", - "single_end": false - }, - "test__evals_e1.nii.gz:md5,ece4e1d0fc03f4bafc882b63285984d3" - ] - ], - "7": [ - [ - { - "id": "test", - "single_end": false - }, - "test__evals_e2.nii.gz:md5,286b867f7ae908fad963a80c9ba74d30" - ] - ], - "8": [ - [ - { - "id": "test", - "single_end": false - }, - "test__evals_e3.nii.gz:md5,1b33203d97ec61d5fd6d1b1a579431ec" - ] - ], - "9": [ - [ - { - "id": "test", - "single_end": false - }, - "test__fa.nii.gz:md5,9bb468c2186f77775d70ebb17ec33a07" - ] - ], - "ad": [ - [ - { - "id": "test", - "single_end": false - }, - "test__ad.nii.gz:md5,ece4e1d0fc03f4bafc882b63285984d3" - ] - ], - "evals": [ - [ - { - "id": "test", - "single_end": false - }, - "test__evals.nii.gz:md5,464d861a0ddda845824b8a4c778d1b6b" - ] - ], - "evals_e1": [ - [ - { - "id": "test", - "single_end": false - }, - "test__evals_e1.nii.gz:md5,ece4e1d0fc03f4bafc882b63285984d3" - ] - ], - "evals_e2": [ - [ - { - "id": "test", - "single_end": false - }, - "test__evals_e2.nii.gz:md5,286b867f7ae908fad963a80c9ba74d30" - ] - ], - "evals_e3": [ - [ - { - "id": "test", - "single_end": false - }, - "test__evals_e3.nii.gz:md5,1b33203d97ec61d5fd6d1b1a579431ec" - ] - ], - "evecs": [ - [ - { - "id": "test", - "single_end": false - }, - "test__evecs.nii.gz:md5,12a42297c1c257336f1b5cb04cd18a45" - ] - ], - "evecs_v1": [ - [ - { - "id": "test", - "single_end": false - }, - "test__evecs_v1.nii.gz:md5,b9b02ffa0ba41ec5e9e52f18c7741f18" - ] - ], - "evecs_v2": [ - [ - { - "id": "test", - "single_end": false - }, - "test__evecs_v2.nii.gz:md5,2189cde6872fb140683a1cd6c5eb1e9e" - ] - ], - "evecs_v3": [ - [ - { - "id": "test", - "single_end": false - }, - "test__evecs_v3.nii.gz:md5,af227812521827a9064e3a8596fffcda" - ] - ], - "fa": [ - [ - { - "id": "test", - "single_end": false - }, - "test__fa.nii.gz:md5,9bb468c2186f77775d70ebb17ec33a07" - ] - ], - "ga": [ - [ - { - "id": "test", - "single_end": false - }, - "test__ga.nii.gz:md5,209ab956ff7e59217db0929c5dff08fa" - ] - ], - "md": [ - [ - { - "id": "test", - "single_end": false - }, - "test__md.nii.gz:md5,d9a6ca6d7ad205b8ec0a90f0db4c53d9" - ] - ], - "mode": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mode.nii.gz:md5,015a1e5541e9fbb720e1c4110ebbcc46" - ] - ], - "nonphysical": [ - [ - { - "id": "test", - "single_end": false - }, - "test__nonphysical.nii.gz:md5,7da6de5ad6e7c37518f9f3962f066f89" - ] - ], - "norm": [ - [ - { - "id": "test", - "single_end": false - }, - "test__norm.nii.gz:md5,9b90f4e4af148a4d0395596fb48b5bef" - ] - ], - "pulsation_std_dwi": [ - - ], - "rd": [ - [ - { - "id": "test", - "single_end": false - }, - "test__rd.nii.gz:md5,d33a7089844a53184c0548cdf8899efa" - ] - ], - "residual": [ - [ - { - "id": "test", - "single_end": false - }, - "test__residual.nii.gz:md5,4d91b617b09018cdc3feb07256665d1b" - ] - ], - "residual_iqr_residuals": [ - [ - { - "id": "test", - "single_end": false - }, - "test__residual_iqr_residuals.npy:md5,4a71d46303bb3ac67088fe5cdaa5694a" - ] - ], - "residual_mean_residuals": [ - [ - { - "id": "test", - "single_end": false - }, - "test__residual_mean_residuals.npy:md5,2247858eaf51c6e973649418f8721477" - ] - ], - "residual_q1_residuals": [ - [ - { - "id": "test", - "single_end": false - }, - "test__residual_q1_residuals.npy:md5,4a71d46303bb3ac67088fe5cdaa5694a" - ] - ], - "residual_q3_residuals": [ - [ - { - "id": "test", - "single_end": false - }, - "test__residual_q3_residuals.npy:md5,4a71d46303bb3ac67088fe5cdaa5694a" - ] - ], - "residual_residuals_stats": [ - [ - { - "id": "test", - "single_end": false - }, - "test__residual_residuals_stats.png:md5,18ce14e9e554c8f5fb1cf0c87af36f9f" - ] - ], - "residual_std_residuals": [ - [ - { - "id": "test", - "single_end": false - }, - "test__residual_std_residuals.npy:md5,5e526c12b8a13b611bd1b2e00d4e1448" - ] - ], - "rgb": [ - [ - { - "id": "test", - "single_end": false - }, - "test__rgb.nii.gz:md5,601b67930e79dbf23dfaeb5aafe6f3e7" - ] - ], - "tensor": [ - [ - { - "id": "test", - "single_end": false - }, - "test__tensor.nii.gz:md5,9eac2b7afe5db2d65650f1307e3b8166" - ] - ], - "versions": [ - "versions.yml:md5,f057a83131297624fb6d9db93df8d749" + "test__ad.nii.gz:md5,9aef42f05ef76cda519c1bf1a4d09e5a", + "test__evecs.nii.gz:md5,5382bf25d965b3d08b1779b3c26542f3", + "test__evecs_v1.nii.gz:md5,b3aafa3d64ab5189adbb1dd449aea59b", + "test__evecs_v2.nii.gz:md5,de7388d34e37e843e39d7b39837fa4aa", + "test__evecs_v3.nii.gz:md5,516d14d6647a03f4a2bd7f51cae20fce", + "test__evals.nii.gz:md5,b5b6e6a3c13b72a89f4626169dc791a8", + "test__evals_e1.nii.gz:md5,9aef42f05ef76cda519c1bf1a4d09e5a", + "test__evals_e2.nii.gz:md5,d3b5247e8d017e737a3f32ccf6944a32", + "test__evals_e3.nii.gz:md5,e749580da032647acf62dfb9405bcbda", + "test__fa.nii.gz:md5,f17769290198fa8b258b228c591a799a", + "test__ga.nii.gz:md5,8ce650bf62a5ff0979d29020ae4e3fa0", + "test__rgb.nii.gz:md5,00f60c043c956b0e95393071a493df37", + "test__md.nii.gz:md5,12baefb237c2b972cf0c6980b0c10681", + "test__mode.nii.gz:md5,f6722dd9ae95c74358fd17dfa214f354", + "test__norm.nii.gz:md5,69399c44ee62d1c52e271f39a1bac4be", + "test__rd.nii.gz:md5,02afa7a113d7946f3a36a0365c1d5f26", + "test__tensor.nii.gz:md5,91a3c8d626ffa8c99495a058b84eead0", + "test__nonphysical.nii.gz:md5,63905c6dc26e33011608bba5f2c0e2f9", + "test__pulsation_std_dwi.nii.gz:md5,fedf3ac5e312d43791269a9e4a18f48c", + "test__residual.nii.gz:md5,eccbda5e154711cba41b3afc1365326d", + [ + [ + { + "id": "test", + "single_end": false + }, + "test__residual_iqr_residuals.npy:md5,4a71d46303bb3ac67088fe5cdaa5694a" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test__residual_mean_residuals.npy:md5,2247858eaf51c6e973649418f8721477" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test__residual_q1_residuals.npy:md5,4a71d46303bb3ac67088fe5cdaa5694a" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test__residual_q3_residuals.npy:md5,4a71d46303bb3ac67088fe5cdaa5694a" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test__residual_residuals_stats.png:md5,18ce14e9e554c8f5fb1cf0c87af36f9f" + ] + ], + [ + [ + { + "id": "test", + "single_end": false + }, + "test__residual_std_residuals.npy:md5,5e526c12b8a13b611bd1b2e00d4e1448" ] - } + ], + [ + "versions.yml:md5,f057a83131297624fb6d9db93df8d749" + ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0-rc1", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-01T19:11:59.341747" + "timestamp": "2024-08-26T14:58:17.511641" } } \ No newline at end of file diff --git a/nf-test.config b/nf-test.config index 48191ceb..3bc9fadf 100755 --- a/nf-test.config +++ b/nf-test.config @@ -15,6 +15,7 @@ config { plugins { repository "https://raw.githubusercontent.com/scilus/nf-scil/main/plugins.json" + repository "./plugins.json" load "nft-nifti@0.0.1" } diff --git a/plugins.json b/plugins.json index 7e1e3613..43894708 100644 --- a/plugins.json +++ b/plugins.json @@ -2,7 +2,7 @@ { "id": "nft-nifti", "latest": "0.0.1", - "url": "https://github.com/scilus/nft-nifti", + "url": "https://github.com/AlexVCaron/nft-nifti", "github": "scilus/nft-nifti", "description": "Provides support for NIFTI files.", "author": "Arnaud Boré", @@ -10,7 +10,7 @@ "releases": [ { "version": "0.0.1", - "url": "https://github.com/scilus/nft-nifti/releases/download/0.0.1/nft-nifti-0.0.1.jar" + "url": "https://github.com/AlexVCaron/nft-nifti/releases/download/0.0.1/nft-nifti-0.0.1.jar" } ] }