diff --git a/modules/nf-neuro/image/resample/main.nf b/modules/nf-neuro/image/resample/main.nf index c9c845e8..b1e07f5a 100755 --- a/modules/nf-neuro/image/resample/main.nf +++ b/modules/nf-neuro/image/resample/main.nf @@ -1,10 +1,11 @@ process IMAGE_RESAMPLE { tag "$meta.id" label 'process_single' + label 'process_high_memory' container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://scil.usherbrooke.ca/containers/scilus_2.0.1.sif': - 'scilus/scilus:2.0.1' }" + 'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif': + 'scilus/scilus:2.0.2' }" input: tuple val(meta), path(image), path(ref) /* optional, input = [] */ @@ -18,6 +19,7 @@ process IMAGE_RESAMPLE { script: def prefix = task.ext.prefix ?: "${meta.id}" + def suffix = task.ext.suffix ? "${task.ext.first_suffix}_resampled" : "resampled" def reference = "$ref" ? "--ref $ref" : "" def voxel_size = task.ext.voxel_size ? "--voxel_size " + task.ext.voxel_size : "" def volume_size = task.ext.volume_size ? "--volume_size " + task.ext.volume_size : "" @@ -31,28 +33,28 @@ process IMAGE_RESAMPLE { export OMP_NUM_THREADS=1 export OPENBLAS_NUM_THREADS=1 - scil_volume_resample.py $image ${prefix}__resampled.nii.gz \ + scil_volume_resample.py $image ${prefix}_${suffix}.nii.gz \ $voxel_size $volume_size $reference $iso_min \ $f $enforce_dimensions $interp - cat <<-END_VERSIONS > versions.yml "${task.process}": - scilpy: 2.0.1 + scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2) END_VERSIONS """ stub: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" + def suffix = task.ext.suffix ? "${task.ext.first_suffix}_resampled" : "resampled" """ scil_volume_resample.py -h - touch ${prefix}__resampled.nii.gz + touch ${prefix}_${suffix}.nii.gz cat <<-END_VERSIONS > versions.yml "${task.process}": - scilpy: 2.0.1 + scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2) END_VERSIONS """ } diff --git a/modules/nf-neuro/image/resample/meta.yml b/modules/nf-neuro/image/resample/meta.yml index 112c6ae6..83aabf09 100755 --- a/modules/nf-neuro/image/resample/meta.yml +++ b/modules/nf-neuro/image/resample/meta.yml @@ -5,7 +5,7 @@ keywords: - resample - nifti - volume - - Scilpy + - scilpy tools: - "scilpy": description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox." diff --git a/modules/nf-neuro/image/resample/tests/main.nf.test.snap b/modules/nf-neuro/image/resample/tests/main.nf.test.snap index 5e74bfe7..8d77f230 100644 --- a/modules/nf-neuro/image/resample/tests/main.nf.test.snap +++ b/modules/nf-neuro/image/resample/tests/main.nf.test.snap @@ -8,11 +8,11 @@ "id": "test", "single_end": false }, - "test__resampled.nii.gz:md5,f3164907d16ceabf606a03ea0efd3a2f" + "test_resampled.nii.gz:md5,f3164907d16ceabf606a03ea0efd3a2f" ] ], "1": [ - "versions.yml:md5,f2c9fb731758ad9909571d60a85fa792" + "versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645" ], "image": [ [ @@ -20,19 +20,19 @@ "id": "test", "single_end": false }, - "test__resampled.nii.gz:md5,f3164907d16ceabf606a03ea0efd3a2f" + "test_resampled.nii.gz:md5,f3164907d16ceabf606a03ea0efd3a2f" ] ], "versions": [ - "versions.yml:md5,f2c9fb731758ad9909571d60a85fa792" + "versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-08T12:39:51.794554" + "timestamp": "2024-10-24T15:30:19.061192" }, "image - resample - nn": { "content": [ @@ -43,11 +43,11 @@ "id": "test", "single_end": false }, - "test__resampled.nii.gz:md5,8d3e1c9552673b1ce60bc4d090198564" + "test_resampled.nii.gz:md5,8d3e1c9552673b1ce60bc4d090198564" ] ], "1": [ - "versions.yml:md5,f2c9fb731758ad9909571d60a85fa792" + "versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645" ], "image": [ [ @@ -55,19 +55,19 @@ "id": "test", "single_end": false }, - "test__resampled.nii.gz:md5,8d3e1c9552673b1ce60bc4d090198564" + "test_resampled.nii.gz:md5,8d3e1c9552673b1ce60bc4d090198564" ] ], "versions": [ - "versions.yml:md5,f2c9fb731758ad9909571d60a85fa792" + "versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-08T12:40:24.002411" + "timestamp": "2024-10-24T15:30:42.725713" }, "image - resample - volsize": { "content": [ @@ -78,11 +78,11 @@ "id": "test", "single_end": false }, - "test__resampled.nii.gz:md5,7c83b666f9fb2d68643a20d1c7ac21d8" + "test_resampled.nii.gz:md5,7c83b666f9fb2d68643a20d1c7ac21d8" ] ], "1": [ - "versions.yml:md5,f2c9fb731758ad9909571d60a85fa792" + "versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645" ], "image": [ [ @@ -90,19 +90,19 @@ "id": "test", "single_end": false }, - "test__resampled.nii.gz:md5,7c83b666f9fb2d68643a20d1c7ac21d8" + "test_resampled.nii.gz:md5,7c83b666f9fb2d68643a20d1c7ac21d8" ] ], "versions": [ - "versions.yml:md5,f2c9fb731758ad9909571d60a85fa792" + "versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-08T12:39:35.764922" + "timestamp": "2024-10-24T15:30:07.1626" }, "image - resample - voxsize": { "content": [ @@ -113,11 +113,11 @@ "id": "test", "single_end": false }, - "test__resampled.nii.gz:md5,6ffdabab138186db2dab6f98ea6e9ffb" + "test_resampled.nii.gz:md5,6ffdabab138186db2dab6f98ea6e9ffb" ] ], "1": [ - "versions.yml:md5,f2c9fb731758ad9909571d60a85fa792" + "versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645" ], "image": [ [ @@ -125,19 +125,19 @@ "id": "test", "single_end": false }, - "test__resampled.nii.gz:md5,6ffdabab138186db2dab6f98ea6e9ffb" + "test_resampled.nii.gz:md5,6ffdabab138186db2dab6f98ea6e9ffb" ] ], "versions": [ - "versions.yml:md5,f2c9fb731758ad9909571d60a85fa792" + "versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-08T12:39:18.016911" + "timestamp": "2024-10-24T15:29:55.01735" }, "image - resample - ref": { "content": [ @@ -148,11 +148,11 @@ "id": "test", "single_end": false }, - "test__resampled.nii.gz:md5,0a45d21ff294fda2e41c620cf83d0406" + "test_resampled.nii.gz:md5,0a45d21ff294fda2e41c620cf83d0406" ] ], "1": [ - "versions.yml:md5,f2c9fb731758ad9909571d60a85fa792" + "versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645" ], "image": [ [ @@ -160,18 +160,18 @@ "id": "test", "single_end": false }, - "test__resampled.nii.gz:md5,0a45d21ff294fda2e41c620cf83d0406" + "test_resampled.nii.gz:md5,0a45d21ff294fda2e41c620cf83d0406" ] ], "versions": [ - "versions.yml:md5,f2c9fb731758ad9909571d60a85fa792" + "versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645" ] } ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-05-08T12:40:07.720638" + "timestamp": "2024-10-24T15:30:31.018615" } } \ No newline at end of file diff --git a/subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test.snap b/subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test.snap index 60fb0c25..c399df6c 100644 --- a/subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test.snap +++ b/subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test.snap @@ -13,29 +13,29 @@ [ "versions.yml:md5,0280006ceecc575513278292734ffb27", "versions.yml:md5,3340c4b5e56ca52f7342be3c9044eb47", - "versions.yml:md5,4d981a0200b8820dd789f135a9dd320f", "versions.yml:md5,5dce7a8c0b0d6b91ef7826f88c86370e", + "versions.yml:md5,7ddf2e98f59b19c9b933670550f26ad7", "versions.yml:md5,962f76092c8795ce5e6d768304e2d230", "versions.yml:md5,b4c068383da080f871c90828b1de0082", "versions.yml:md5,c15ba5efd24564dba4710b6da8c4b791", - "versions.yml:md5,d1ae2ca80502bf88c4b1c4a42fba6ced", "versions.yml:md5,d3010f785c88ee5946806a8a758e7efb", "versions.yml:md5,d68fe3399120f84f1add62181708780b", + "versions.yml:md5,ea5858879452a59bb355228ae7f38111", "versions.yml:md5,f041502e22449973d84ac1c618e8ebf9" ], "test_b0.nii.gz", - "test__resampled.nii.gz", + "test_resampled.nii.gz", "test__dwi_eddy_corrected.bvec", "test__image_boundingBox.pkl", "test__image_n4.nii.gz", - "test__resampled.nii.gz", + "test_resampled.nii.gz", "test__dwi_corrected.nii.gz" ], "meta": { - "nf-test": "0.9.0-rc1", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-05T18:15:01.714505" + "timestamp": "2024-10-24T15:39:59.890109" }, "preproc_dwi_rev_b0": { "content": [ @@ -51,28 +51,28 @@ [ "versions.yml:md5,0280006ceecc575513278292734ffb27", "versions.yml:md5,3340c4b5e56ca52f7342be3c9044eb47", - "versions.yml:md5,4d981a0200b8820dd789f135a9dd320f", "versions.yml:md5,5dce7a8c0b0d6b91ef7826f88c86370e", + "versions.yml:md5,7ddf2e98f59b19c9b933670550f26ad7", "versions.yml:md5,962f76092c8795ce5e6d768304e2d230", "versions.yml:md5,b4c068383da080f871c90828b1de0082", "versions.yml:md5,c15ba5efd24564dba4710b6da8c4b791", - "versions.yml:md5,d1ae2ca80502bf88c4b1c4a42fba6ced", "versions.yml:md5,d3010f785c88ee5946806a8a758e7efb", + "versions.yml:md5,ea5858879452a59bb355228ae7f38111", "versions.yml:md5,f041502e22449973d84ac1c618e8ebf9" ], "test_b0.nii.gz", - "test__resampled.nii.gz", + "test_resampled.nii.gz", "test__dwi_eddy_corrected.bvec", "test__image_boundingBox.pkl", "test__image_n4.nii.gz", - "test__resampled.nii.gz", + "test_resampled.nii.gz", "test__dwi_corrected.nii.gz" ], "meta": { - "nf-test": "0.9.0-rc1", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-05T18:10:40.247701" + "timestamp": "2024-10-24T15:35:59.573081" }, "preproc_dwi_all_options": { "content": [ @@ -88,27 +88,27 @@ [ "versions.yml:md5,0280006ceecc575513278292734ffb27", "versions.yml:md5,3340c4b5e56ca52f7342be3c9044eb47", - "versions.yml:md5,4d981a0200b8820dd789f135a9dd320f", "versions.yml:md5,5dce7a8c0b0d6b91ef7826f88c86370e", + "versions.yml:md5,7ddf2e98f59b19c9b933670550f26ad7", "versions.yml:md5,962f76092c8795ce5e6d768304e2d230", "versions.yml:md5,b4c068383da080f871c90828b1de0082", "versions.yml:md5,c15ba5efd24564dba4710b6da8c4b791", - "versions.yml:md5,d1ae2ca80502bf88c4b1c4a42fba6ced", "versions.yml:md5,d68fe3399120f84f1add62181708780b", + "versions.yml:md5,ea5858879452a59bb355228ae7f38111", "versions.yml:md5,f041502e22449973d84ac1c618e8ebf9" ], "test_b0.nii.gz", - "test__resampled.nii.gz", + "test_resampled.nii.gz", "test__dwi_eddy_corrected.bvec", "test__image_boundingBox.pkl", "test__image_n4.nii.gz", - "test__resampled.nii.gz", + "test_resampled.nii.gz", "test__dwi_corrected.nii.gz" ], "meta": { - "nf-test": "0.9.0-rc1", + "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-05T18:20:22.568596" + "timestamp": "2024-10-24T15:44:27.839939" } } \ No newline at end of file diff --git a/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test b/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test index 85724c0c..3e8ca62c 100644 --- a/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test +++ b/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test @@ -22,7 +22,7 @@ nextflow_workflow { script "../../load_test_data/main.nf" process { """ - input[0] = Channel.from( [ "antsbet.zip" , "others.zip" ] ) + input[0] = Channel.from( [ "antsbet.zip" , "T1w.zip" ] ) input[1] = "test.load-test-data" """ } @@ -37,12 +37,12 @@ nextflow_workflow { ch_split_test_data = LOAD_DATA.out.test_data_directory .branch{ antsbet: it.simpleName == "antsbet" - others: it.simpleName == "others" + t1w: it.simpleName == "T1w" } - input[0] = ch_split_test_data.antsbet.map{ + input[0] = ch_split_test_data.t1w.map{ test_data_directory -> [ [ id:'test', single_end:false ], - file("\${test_data_directory}/t1_unaligned.nii.gz") + file("\${test_data_directory}/T1w.nii.gz") ]} input[1] = ch_split_test_data.antsbet.map{ test_data_directory -> [ @@ -54,18 +54,18 @@ nextflow_workflow { [ id:'test', single_end:false ], file("\${test_data_directory}/t1_brain_probability_map.nii.gz") ]} - input[3] = ch_split_test_data.others.map{ + input[3] = ch_split_test_data.t1w.map{ test_data_directory -> [ [ id:'test', single_end:false ], [] ]} - input[4] = ch_split_test_data.others.map{ + input[4] = ch_split_test_data.t1w.map{ test_data_directory -> [ [ id:'test', single_end:false ], [], [] ]} - input[5] = ch_split_test_data.others.map{ + input[5] = ch_split_test_data.t1w.map{ test_data_directory -> [ [ id:'test', single_end:false ], [] @@ -106,38 +106,38 @@ nextflow_workflow { ch_split_test_data = LOAD_DATA.out.test_data_directory .branch{ antsbet: it.simpleName == "antsbet" - others: it.simpleName == "others" + t1w: it.simpleName == "T1w" } - input[0] = ch_split_test_data.antsbet.map{ + input[0] = ch_split_test_data.t1w.map{ test_data_directory -> [ [ id:'test', single_end:false ], - file("\${test_data_directory}/t1_unaligned.nii.gz") + file("\${test_data_directory}/T1w.nii.gz") ]} input[1] = ch_split_test_data.antsbet.map{ test_data_directory -> [ [ id:'test', single_end:false ], - file("\${test_data_directory}/t1_template.nii.gz") + [] ]} input[2] = ch_split_test_data.antsbet.map{ test_data_directory -> [ [ id:'test', single_end:false ], - file("\${test_data_directory}/t1_brain_probability_map.nii.gz") + [] ]} - input[3] = ch_split_test_data.antsbet.map{ + input[3] = ch_split_test_data.t1w.map{ test_data_directory -> [ [ id:'test', single_end:false ], - file("\${test_data_directory}/t1_unaligned_brainmask.nii.gz") + file("\${test_data_directory}/T1w_mask.nii.gz") ]} - input[4] = ch_split_test_data.others.map{ + input[4] = ch_split_test_data.t1w.map{ test_data_directory -> [ [ id:'test', single_end:false ], [], [] ]} - input[5] = ch_split_test_data.antsbet.map{ + input[5] = ch_split_test_data.t1w.map{ test_data_directory -> [ [ id:'test', single_end:false ], - file("\${test_data_directory}/t1_unaligned.nii.gz") + file("\${test_data_directory}/T1w.nii.gz") ]} input[6] = ch_split_test_data.antsbet.map{ test_data_directory -> [ @@ -175,12 +175,12 @@ nextflow_workflow { ch_split_test_data = LOAD_DATA.out.test_data_directory .branch{ antsbet: it.simpleName == "antsbet" - others: it.simpleName == "others" + t1w: it.simpleName == "T1w" } - input[0] = ch_split_test_data.antsbet.map{ + input[0] = ch_split_test_data.t1w.map{ test_data_directory -> [ [ id:'test', single_end:false ], - file("\${test_data_directory}/t1_unaligned.nii.gz") + file("\${test_data_directory}/T1w.nii.gz") ]} input[1] = ch_split_test_data.antsbet.map{ test_data_directory -> [ @@ -197,7 +197,7 @@ nextflow_workflow { [ id:'test', single_end:false ], [] ]} - input[4] = ch_split_test_data.others.map{ + input[4] = ch_split_test_data.t1w.map{ test_data_directory -> [ [ id:'test', single_end:false ], [], diff --git a/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap b/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap index 3a4c620d..5a5bff44 100644 --- a/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap +++ b/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap @@ -1,101 +1,101 @@ { "preproc_t1_synthbet": { "content": [ - 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"timestamp": "2024-09-29T22:11:22.559727" + "timestamp": "2024-10-28T11:47:30.704886581" } } \ No newline at end of file diff --git a/subworkflows/nf-neuro/preproc_t1/tests/nextflow_2.config b/subworkflows/nf-neuro/preproc_t1/tests/nextflow_2.config index f4a30695..8342c09b 100644 --- a/subworkflows/nf-neuro/preproc_t1/tests/nextflow_2.config +++ b/subworkflows/nf-neuro/preproc_t1/tests/nextflow_2.config @@ -7,4 +7,10 @@ process { ext.output_bbox = true ext.first_suffix = "t1" } + withName: "BETCROP_SYNTHBET" { + memory = "8G" + ext.nocsf = true + } } + +params.run_synthbet = true