diff --git a/modules/nf-scil/segmentation/fastseg/tests/main.nf.test b/modules/nf-scil/segmentation/fastseg/tests/main.nf.test index a081ce87..9114b5e9 100644 --- a/modules/nf-scil/segmentation/fastseg/tests/main.nf.test +++ b/modules/nf-scil/segmentation/fastseg/tests/main.nf.test @@ -20,7 +20,7 @@ nextflow_process { script "../../../../../subworkflows/nf-scil/load_test_data/main.nf" process { """ - input[0] = Channel.from( [ "heavy.zip" ] ) + input[0] = Channel.from( [ "T1w.zip" ] ) input[1] = "test.load-test-data" """ } @@ -34,7 +34,7 @@ nextflow_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", checkIfExists: true,), + file("\${test_data_directory}/T1w.nii.gz", checkIfExists: true,), [] ] } @@ -45,7 +45,15 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + niftiMD5SUM(process.out.wm_mask.get(0).get(1)), + niftiMD5SUM(process.out.gm_mask.get(0).get(1)), + niftiMD5SUM(process.out.csf_mask.get(0).get(1)), + niftiMD5SUM(process.out.wm_map.get(0).get(1)), + niftiMD5SUM(process.out.gm_map.get(0).get(1)), + niftiMD5SUM(process.out.csf_map.get(0).get(1)), + process.out.versions + ).match() } ) } } @@ -56,8 +64,8 @@ nextflow_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", checkIfExists: true,), - file("\${test_data_directory}/anat/anat_mask.nii.gz", checkIfExists: true) + file("\${test_data_directory}/T1w.nii.gz", checkIfExists: true,), + file("\${test_data_directory}/T1w_mask.nii.gz", checkIfExists: true) ] } """ @@ -67,7 +75,15 @@ nextflow_process { then { assertAll( { assert process.success }, - { assert snapshot(process.out).match() } + { assert snapshot( + niftiMD5SUM(process.out.wm_mask.get(0).get(1)), + niftiMD5SUM(process.out.gm_mask.get(0).get(1)), + niftiMD5SUM(process.out.csf_mask.get(0).get(1)), + niftiMD5SUM(process.out.wm_map.get(0).get(1)), + niftiMD5SUM(process.out.gm_map.get(0).get(1)), + niftiMD5SUM(process.out.csf_map.get(0).get(1)), + process.out.versions + ).match() } ) } } diff --git a/modules/nf-scil/segmentation/fastseg/tests/main.nf.test.snap b/modules/nf-scil/segmentation/fastseg/tests/main.nf.test.snap index 7ae441af..7778861a 100644 --- a/modules/nf-scil/segmentation/fastseg/tests/main.nf.test.snap +++ b/modules/nf-scil/segmentation/fastseg/tests/main.nf.test.snap @@ -1,252 +1,38 @@ { "segmentation - fastseg - lesion": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_wm.nii.gz:md5,2b2ced42fcf870d68ff44bf90d2701d4" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_gm.nii.gz:md5,39396421c6d1d32ea7943a5ec7a49dce" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_csf.nii.gz:md5,d0fbc088059f17faff38fbcd33257d27" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_wm.nii.gz:md5,1d5a9655d4e3c832b14c83e9424b00fc" - ] - ], - "4": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_gm.nii.gz:md5,f7e51eb14af645c687db5d2c6a4f5bf4" - ] - ], - "5": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_csf.nii.gz:md5,9c14d8f70e69d641d9c214d0d52b3663" - ] - ], - "6": [ - "versions.yml:md5,d42da2620c5aa82292375b0f9d8d7092" - ], - "csf_map": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_csf.nii.gz:md5,9c14d8f70e69d641d9c214d0d52b3663" - ] - ], - "csf_mask": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_csf.nii.gz:md5,d0fbc088059f17faff38fbcd33257d27" - ] - ], - "gm_map": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_gm.nii.gz:md5,f7e51eb14af645c687db5d2c6a4f5bf4" - ] - ], - "gm_mask": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_gm.nii.gz:md5,39396421c6d1d32ea7943a5ec7a49dce" - ] - ], - "versions": [ - "versions.yml:md5,d42da2620c5aa82292375b0f9d8d7092" - ], - "wm_map": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_wm.nii.gz:md5,1d5a9655d4e3c832b14c83e9424b00fc" - ] - ], - "wm_mask": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_wm.nii.gz:md5,2b2ced42fcf870d68ff44bf90d2701d4" - ] - ] - } + "test__mask_wm.nii.gz:md5:header,18e02970ee42367e0ee9f81b36cde160,data,e4d00ba5559d32119050e6afe77b627c", + "test__mask_gm.nii.gz:md5:header,cb2d88714675fc7d8c450de4db5227c6,data,d713974dbe87760182112e10f96a7f82", + "test__mask_csf.nii.gz:md5:header,cb2d88714675fc7d8c450de4db5227c6,data,29599fab55e3ee75318cef36563684a4", + "test__map_wm.nii.gz:md5:header,58dc3623694060dace951ba8073d5e01,data,62a268dbc74814d62ed9f9596b5a72e5", + "test__map_gm.nii.gz:md5:header,58dc3623694060dace951ba8073d5e01,data,420e7664f81a5899f7007f71c08f28d8", + "test__map_csf.nii.gz:md5:header,58dc3623694060dace951ba8073d5e01,data,2bde307c6dae36a5fc00eba7a2ca7933", + [ + "versions.yml:md5,d42da2620c5aa82292375b0f9d8d7092" + ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0-rc1", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-17T13:59:58.264241" + "timestamp": "2024-09-04T20:12:08.928978" }, "segmentation - fastseg": { "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_wm.nii.gz:md5,f849e268007a747714e342162f13f631" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_gm.nii.gz:md5,39396421c6d1d32ea7943a5ec7a49dce" - ] - ], - "2": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_csf.nii.gz:md5,d0fbc088059f17faff38fbcd33257d27" - ] - ], - "3": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_wm.nii.gz:md5,1d5a9655d4e3c832b14c83e9424b00fc" - ] - ], - "4": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_gm.nii.gz:md5,f7e51eb14af645c687db5d2c6a4f5bf4" - ] - ], - "5": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_csf.nii.gz:md5,9c14d8f70e69d641d9c214d0d52b3663" - ] - ], - "6": [ - "versions.yml:md5,d42da2620c5aa82292375b0f9d8d7092" - ], - "csf_map": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_csf.nii.gz:md5,9c14d8f70e69d641d9c214d0d52b3663" - ] - ], - "csf_mask": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_csf.nii.gz:md5,d0fbc088059f17faff38fbcd33257d27" - ] - ], - "gm_map": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_gm.nii.gz:md5,f7e51eb14af645c687db5d2c6a4f5bf4" - ] - ], - "gm_mask": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_gm.nii.gz:md5,39396421c6d1d32ea7943a5ec7a49dce" - ] - ], - "versions": [ - "versions.yml:md5,d42da2620c5aa82292375b0f9d8d7092" - ], - "wm_map": [ - [ - { - "id": "test", - "single_end": false - }, - "test__map_wm.nii.gz:md5,1d5a9655d4e3c832b14c83e9424b00fc" - ] - ], - "wm_mask": [ - [ - { - "id": "test", - "single_end": false - }, - "test__mask_wm.nii.gz:md5,f849e268007a747714e342162f13f631" - ] - ] - } + "test__mask_wm.nii.gz:md5:header,cb2d88714675fc7d8c450de4db5227c6,data,08b5c8665f0a07c182eb63f045d01855", + "test__mask_gm.nii.gz:md5:header,cb2d88714675fc7d8c450de4db5227c6,data,d713974dbe87760182112e10f96a7f82", + "test__mask_csf.nii.gz:md5:header,cb2d88714675fc7d8c450de4db5227c6,data,29599fab55e3ee75318cef36563684a4", + "test__map_wm.nii.gz:md5:header,58dc3623694060dace951ba8073d5e01,data,62a268dbc74814d62ed9f9596b5a72e5", + "test__map_gm.nii.gz:md5:header,58dc3623694060dace951ba8073d5e01,data,420e7664f81a5899f7007f71c08f28d8", + "test__map_csf.nii.gz:md5:header,58dc3623694060dace951ba8073d5e01,data,2bde307c6dae36a5fc00eba7a2ca7933", + [ + "versions.yml:md5,d42da2620c5aa82292375b0f9d8d7092" + ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0-rc1", + "nextflow": "24.04.4" }, - "timestamp": "2024-06-13T19:52:04.291343" + "timestamp": "2024-09-04T20:03:24.730234" } } \ No newline at end of file diff --git a/tests/config/test_data.json b/tests/config/test_data.json index f52c60d8..b5201265 100644 --- a/tests/config/test_data.json +++ b/tests/config/test_data.json @@ -48,7 +48,7 @@ "DWIss300-dir8.zip": "ef1335775c9fbf11452c71e01b097282", "DWIss1000-dir32.zip": "c72fd590a3f400278299a068eeffd1d0", "DWIss2000-dir60.zip": "9ad7ccb4e30b39c47f374018db2e6424", - "T1w.zip": "10e27bb2ddd4d01be968a93b2166096c", + "T1w.zip": "8e9cf2beec4595d407732152a19589f5", "dti.zip": "ba866c59fc4d984f626691a6b941fc32", "responses.zip": "1a5b862b91c72740bcce0431a1f9254a", "segmentation.zip": "ab51be6d142ad1a8e30ffb964447d010"