From c91f038c10ab8c851f3e62dc02846a3b32a7b1a6 Mon Sep 17 00:00:00 2001 From: medde Date: Thu, 12 Dec 2024 18:14:34 +0000 Subject: [PATCH 1/8] copy cropvolume --- .../betcrop/cropvolume/environment.yml | 3 - modules/nf-neuro/betcrop/cropvolume/main.nf | 56 ----------- modules/nf-neuro/betcrop/cropvolume/meta.yml | 54 ----------- .../betcrop/cropvolume/tests/main.nf.test | 80 ---------------- .../cropvolume/tests/main.nf.test.snap | 96 ------------------- .../betcrop/cropvolume/tests/nextflow.config | 5 - .../cropvolume/tests/nextflow_bbox.config | 6 -- .../betcrop/cropvolume/tests/tags.yml | 2 - 8 files changed, 302 deletions(-) delete mode 100644 modules/nf-neuro/betcrop/cropvolume/environment.yml delete mode 100755 modules/nf-neuro/betcrop/cropvolume/main.nf delete mode 100755 modules/nf-neuro/betcrop/cropvolume/meta.yml delete mode 100644 modules/nf-neuro/betcrop/cropvolume/tests/main.nf.test delete mode 100644 modules/nf-neuro/betcrop/cropvolume/tests/main.nf.test.snap delete mode 100644 modules/nf-neuro/betcrop/cropvolume/tests/nextflow.config delete mode 100644 modules/nf-neuro/betcrop/cropvolume/tests/nextflow_bbox.config delete mode 100644 modules/nf-neuro/betcrop/cropvolume/tests/tags.yml diff --git a/modules/nf-neuro/betcrop/cropvolume/environment.yml b/modules/nf-neuro/betcrop/cropvolume/environment.yml deleted file mode 100644 index 3adeaf1e..00000000 --- a/modules/nf-neuro/betcrop/cropvolume/environment.yml +++ /dev/null @@ -1,3 +0,0 @@ -channels: [] -dependencies: [] -name: betcrop_cropvolume diff --git a/modules/nf-neuro/betcrop/cropvolume/main.nf b/modules/nf-neuro/betcrop/cropvolume/main.nf deleted file mode 100755 index e8f47015..00000000 --- a/modules/nf-neuro/betcrop/cropvolume/main.nf +++ /dev/null @@ -1,56 +0,0 @@ - -process BETCROP_CROPVOLUME { - tag "$meta.id" - label 'process_single' - - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif': - 'scilus/scilus:2.0.2' }" - - input: - tuple val(meta), path(image), path(bounding_box) - - output: - tuple val(meta), path("*_cropped.nii.gz"), emit: image - tuple val(meta), path("*.pkl") , emit: bounding_box, optional: true - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def prefix = task.ext.prefix ?: "${meta.id}" - - def input_bbox = bounding_box ? "--input_bbox $bounding_box" : "" - def suffix = task.ext.first_suffix ? "${task.ext.first_suffix}_cropped" : "cropped" - def output_bbox = task.ext.output_bbox ? "--output_bbox ${prefix}_${suffix}_bbox.pkl" : "" - - """ - scil_volume_crop.py $image ${prefix}_${suffix}.nii.gz $input_bbox $output_bbox - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2) - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - def suffix = task.ext.first_suffix ? "${task.ext.first_suffix}_cropped" : "cropped" - - """ - scil_volume_crop.py -h - - touch ${prefix}_${suffix}.nii.gz - - if $task.ext.output_bbox; - then - touch ${prefix}_${suffix}_bbox.pkl - fi - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2) - END_VERSIONS - """ -} diff --git a/modules/nf-neuro/betcrop/cropvolume/meta.yml b/modules/nf-neuro/betcrop/cropvolume/meta.yml deleted file mode 100755 index e981e340..00000000 --- a/modules/nf-neuro/betcrop/cropvolume/meta.yml +++ /dev/null @@ -1,54 +0,0 @@ ---- -# yaml-language-server: $schema=https://raw.githubusercontent.com/scilus/nf-neuro/main/modules/meta-schema.json -name: "betcrop_cropvolume" -description: Crop empty planes around the data in a volume -keywords: - - nifti - - crop - - scilpy -tools: - - "scilpy": - description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox." - homepage: "https://github.com/scilus/scilpy.git" - -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - - image: - type: file - description: Nifti image file to crop - pattern: "*.{nii,nii.gz}" - - - bounding_box: - type: file - description: Input bounding box to use to crop the image - pattern: "*.{pkl}" - -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. `[ id:'test', single_end:false ]` - - - image: - type: file - description: Cropped Nifti image file - pattern: "*_cropped.{nii,nii.gz}" - - - bounding_box: - type: file - description: Bouding box defining the limits of the crop - pattern: "*.pkl" - - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" - -authors: - - "@AlexVCaron" diff --git a/modules/nf-neuro/betcrop/cropvolume/tests/main.nf.test b/modules/nf-neuro/betcrop/cropvolume/tests/main.nf.test deleted file mode 100644 index 06333238..00000000 --- a/modules/nf-neuro/betcrop/cropvolume/tests/main.nf.test +++ /dev/null @@ -1,80 +0,0 @@ -nextflow_process { - - name "Test Process BETCROP_CROPVOLUME" - script "../main.nf" - process "BETCROP_CROPVOLUME" - config "./nextflow.config" - - tag "modules" - tag "modules_nfcore" - tag "betcrop" - tag "betcrop/cropvolume" - - tag "subworkflows" - tag "subworkflows/load_test_data" - - setup { - run("LOAD_TEST_DATA", alias: "LOAD_DATA") { - script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf" - process { - """ - input[0] = Channel.from( [ "heavy.zip" ] ) - input[1] = "test.load-test-data" - """ - } - } - } - - test("betcrop - cropvolume") { - - 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() } - ) - } - - } - - test("betcrop - cropvolume - outputbbox") { - - config "./nextflow_bbox.config" - - 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() } - ) - } - - } - -} diff --git a/modules/nf-neuro/betcrop/cropvolume/tests/main.nf.test.snap b/modules/nf-neuro/betcrop/cropvolume/tests/main.nf.test.snap deleted file mode 100644 index ec0dfa70..00000000 --- a/modules/nf-neuro/betcrop/cropvolume/tests/main.nf.test.snap +++ /dev/null @@ -1,96 +0,0 @@ -{ - "betcrop - cropvolume - outputbbox": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test_cropped.nii.gz:md5,93cc10f69b0829409c69bf743e9c95ef" - ] - ], - "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test_cropped_bbox.pkl:md5,d6a03b61669b07683e8c4b21a613f16c" - ] - ], - "2": [ - "versions.yml:md5,3b089d55a1116feffa69d739ced1d99f" - ], - "bounding_box": [ - [ - { - "id": "test", - "single_end": false - }, - "test_cropped_bbox.pkl:md5,d6a03b61669b07683e8c4b21a613f16c" - ] - ], - "image": [ - [ - { - "id": "test", - "single_end": false - }, - "test_cropped.nii.gz:md5,93cc10f69b0829409c69bf743e9c95ef" - ] - ], - "versions": [ - "versions.yml:md5,3b089d55a1116feffa69d739ced1d99f" - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-28T19:30:09.320626173" - }, - "betcrop - cropvolume": { - "content": [ - { - "0": [ - [ - { - "id": "test", - "single_end": false - }, - "test_cropped.nii.gz:md5,93cc10f69b0829409c69bf743e9c95ef" - ] - ], - "1": [ - - ], - "2": [ - "versions.yml:md5,3b089d55a1116feffa69d739ced1d99f" - ], - "bounding_box": [ - - ], - "image": [ - [ - { - "id": "test", - "single_end": false - }, - "test_cropped.nii.gz:md5,93cc10f69b0829409c69bf743e9c95ef" - ] - ], - "versions": [ - "versions.yml:md5,3b089d55a1116feffa69d739ced1d99f" - ] - } - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-10-28T19:30:00.033087617" - } -} \ No newline at end of file diff --git a/modules/nf-neuro/betcrop/cropvolume/tests/nextflow.config b/modules/nf-neuro/betcrop/cropvolume/tests/nextflow.config deleted file mode 100644 index 7a7632ff..00000000 --- a/modules/nf-neuro/betcrop/cropvolume/tests/nextflow.config +++ /dev/null @@ -1,5 +0,0 @@ -process { - withName: "BETCROP_CROPVOLUME" { - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - } -} diff --git a/modules/nf-neuro/betcrop/cropvolume/tests/nextflow_bbox.config b/modules/nf-neuro/betcrop/cropvolume/tests/nextflow_bbox.config deleted file mode 100644 index c998553c..00000000 --- a/modules/nf-neuro/betcrop/cropvolume/tests/nextflow_bbox.config +++ /dev/null @@ -1,6 +0,0 @@ -process { - withName: "BETCROP_CROPVOLUME" { - ext.output_bbox = true - publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - } -} diff --git a/modules/nf-neuro/betcrop/cropvolume/tests/tags.yml b/modules/nf-neuro/betcrop/cropvolume/tests/tags.yml deleted file mode 100644 index d6802302..00000000 --- a/modules/nf-neuro/betcrop/cropvolume/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -betcrop/cropvolume: - - "modules/nf-neuro/betcrop/cropvolume/**" From e251ddb4ea22d76d4501b18018d7679ef249810a Mon Sep 17 00:00:00 2001 From: medde Date: Thu, 12 Dec 2024 18:14:54 +0000 Subject: [PATCH 2/8] copy cropvolume --- .../nf-neuro/image/cropvolume/environment.yml | 3 + modules/nf-neuro/image/cropvolume/main.nf | 56 +++++++++++ modules/nf-neuro/image/cropvolume/meta.yml | 54 +++++++++++ .../image/cropvolume/tests/main.nf.test | 80 ++++++++++++++++ .../image/cropvolume/tests/main.nf.test.snap | 96 +++++++++++++++++++ .../image/cropvolume/tests/nextflow.config | 5 + .../cropvolume/tests/nextflow_bbox.config | 6 ++ .../nf-neuro/image/cropvolume/tests/tags.yml | 2 + 8 files changed, 302 insertions(+) create mode 100644 modules/nf-neuro/image/cropvolume/environment.yml create mode 100755 modules/nf-neuro/image/cropvolume/main.nf create mode 100755 modules/nf-neuro/image/cropvolume/meta.yml create mode 100644 modules/nf-neuro/image/cropvolume/tests/main.nf.test create mode 100644 modules/nf-neuro/image/cropvolume/tests/main.nf.test.snap create mode 100644 modules/nf-neuro/image/cropvolume/tests/nextflow.config create mode 100644 modules/nf-neuro/image/cropvolume/tests/nextflow_bbox.config create mode 100644 modules/nf-neuro/image/cropvolume/tests/tags.yml diff --git a/modules/nf-neuro/image/cropvolume/environment.yml b/modules/nf-neuro/image/cropvolume/environment.yml new file mode 100644 index 00000000..3adeaf1e --- /dev/null +++ b/modules/nf-neuro/image/cropvolume/environment.yml @@ -0,0 +1,3 @@ +channels: [] +dependencies: [] +name: betcrop_cropvolume diff --git a/modules/nf-neuro/image/cropvolume/main.nf b/modules/nf-neuro/image/cropvolume/main.nf new file mode 100755 index 00000000..e8f47015 --- /dev/null +++ b/modules/nf-neuro/image/cropvolume/main.nf @@ -0,0 +1,56 @@ + +process BETCROP_CROPVOLUME { + tag "$meta.id" + label 'process_single' + + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif': + 'scilus/scilus:2.0.2' }" + + input: + tuple val(meta), path(image), path(bounding_box) + + output: + tuple val(meta), path("*_cropped.nii.gz"), emit: image + tuple val(meta), path("*.pkl") , emit: bounding_box, optional: true + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + + def input_bbox = bounding_box ? "--input_bbox $bounding_box" : "" + def suffix = task.ext.first_suffix ? "${task.ext.first_suffix}_cropped" : "cropped" + def output_bbox = task.ext.output_bbox ? "--output_bbox ${prefix}_${suffix}_bbox.pkl" : "" + + """ + scil_volume_crop.py $image ${prefix}_${suffix}.nii.gz $input_bbox $output_bbox + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def suffix = task.ext.first_suffix ? "${task.ext.first_suffix}_cropped" : "cropped" + + """ + scil_volume_crop.py -h + + touch ${prefix}_${suffix}.nii.gz + + if $task.ext.output_bbox; + then + touch ${prefix}_${suffix}_bbox.pkl + fi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2) + END_VERSIONS + """ +} diff --git a/modules/nf-neuro/image/cropvolume/meta.yml b/modules/nf-neuro/image/cropvolume/meta.yml new file mode 100755 index 00000000..e981e340 --- /dev/null +++ b/modules/nf-neuro/image/cropvolume/meta.yml @@ -0,0 +1,54 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/scilus/nf-neuro/main/modules/meta-schema.json +name: "betcrop_cropvolume" +description: Crop empty planes around the data in a volume +keywords: + - nifti + - crop + - scilpy +tools: + - "scilpy": + description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox." + homepage: "https://github.com/scilus/scilpy.git" + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + + - image: + type: file + description: Nifti image file to crop + pattern: "*.{nii,nii.gz}" + + - bounding_box: + type: file + description: Input bounding box to use to crop the image + pattern: "*.{pkl}" + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + + - image: + type: file + description: Cropped Nifti image file + pattern: "*_cropped.{nii,nii.gz}" + + - bounding_box: + type: file + description: Bouding box defining the limits of the crop + pattern: "*.pkl" + + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + +authors: + - "@AlexVCaron" diff --git a/modules/nf-neuro/image/cropvolume/tests/main.nf.test b/modules/nf-neuro/image/cropvolume/tests/main.nf.test new file mode 100644 index 00000000..06333238 --- /dev/null +++ b/modules/nf-neuro/image/cropvolume/tests/main.nf.test @@ -0,0 +1,80 @@ +nextflow_process { + + name "Test Process BETCROP_CROPVOLUME" + script "../main.nf" + process "BETCROP_CROPVOLUME" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "betcrop" + tag "betcrop/cropvolume" + + tag "subworkflows" + tag "subworkflows/load_test_data" + + setup { + run("LOAD_TEST_DATA", alias: "LOAD_DATA") { + script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf" + process { + """ + input[0] = Channel.from( [ "heavy.zip" ] ) + input[1] = "test.load-test-data" + """ + } + } + } + + test("betcrop - cropvolume") { + + 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() } + ) + } + + } + + test("betcrop - cropvolume - outputbbox") { + + config "./nextflow_bbox.config" + + 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() } + ) + } + + } + +} diff --git a/modules/nf-neuro/image/cropvolume/tests/main.nf.test.snap b/modules/nf-neuro/image/cropvolume/tests/main.nf.test.snap new file mode 100644 index 00000000..ec0dfa70 --- /dev/null +++ b/modules/nf-neuro/image/cropvolume/tests/main.nf.test.snap @@ -0,0 +1,96 @@ +{ + "betcrop - cropvolume - outputbbox": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_cropped.nii.gz:md5,93cc10f69b0829409c69bf743e9c95ef" + ] + ], + "1": [ + [ + { + "id": "test", + "single_end": false + }, + "test_cropped_bbox.pkl:md5,d6a03b61669b07683e8c4b21a613f16c" + ] + ], + "2": [ + "versions.yml:md5,3b089d55a1116feffa69d739ced1d99f" + ], + "bounding_box": [ + [ + { + "id": "test", + "single_end": false + }, + "test_cropped_bbox.pkl:md5,d6a03b61669b07683e8c4b21a613f16c" + ] + ], + "image": [ + [ + { + "id": "test", + "single_end": false + }, + "test_cropped.nii.gz:md5,93cc10f69b0829409c69bf743e9c95ef" + ] + ], + "versions": [ + "versions.yml:md5,3b089d55a1116feffa69d739ced1d99f" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-28T19:30:09.320626173" + }, + "betcrop - cropvolume": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test_cropped.nii.gz:md5,93cc10f69b0829409c69bf743e9c95ef" + ] + ], + "1": [ + + ], + "2": [ + "versions.yml:md5,3b089d55a1116feffa69d739ced1d99f" + ], + "bounding_box": [ + + ], + "image": [ + [ + { + "id": "test", + "single_end": false + }, + "test_cropped.nii.gz:md5,93cc10f69b0829409c69bf743e9c95ef" + ] + ], + "versions": [ + "versions.yml:md5,3b089d55a1116feffa69d739ced1d99f" + ] + } + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-10-28T19:30:00.033087617" + } +} \ No newline at end of file diff --git a/modules/nf-neuro/image/cropvolume/tests/nextflow.config b/modules/nf-neuro/image/cropvolume/tests/nextflow.config new file mode 100644 index 00000000..7a7632ff --- /dev/null +++ b/modules/nf-neuro/image/cropvolume/tests/nextflow.config @@ -0,0 +1,5 @@ +process { + withName: "BETCROP_CROPVOLUME" { + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + } +} diff --git a/modules/nf-neuro/image/cropvolume/tests/nextflow_bbox.config b/modules/nf-neuro/image/cropvolume/tests/nextflow_bbox.config new file mode 100644 index 00000000..c998553c --- /dev/null +++ b/modules/nf-neuro/image/cropvolume/tests/nextflow_bbox.config @@ -0,0 +1,6 @@ +process { + withName: "BETCROP_CROPVOLUME" { + ext.output_bbox = true + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + } +} diff --git a/modules/nf-neuro/image/cropvolume/tests/tags.yml b/modules/nf-neuro/image/cropvolume/tests/tags.yml new file mode 100644 index 00000000..d6802302 --- /dev/null +++ b/modules/nf-neuro/image/cropvolume/tests/tags.yml @@ -0,0 +1,2 @@ +betcrop/cropvolume: + - "modules/nf-neuro/betcrop/cropvolume/**" From 7927191d9f5323be15d69e99c49833d98911fc1e Mon Sep 17 00:00:00 2001 From: medde Date: Thu, 12 Dec 2024 18:35:56 +0000 Subject: [PATCH 3/8] update betcrop to image in all scripts --- .../nf-neuro/image/cropvolume/environment.yml | 2 +- modules/nf-neuro/image/cropvolume/main.nf | 2 +- modules/nf-neuro/image/cropvolume/meta.yml | 2 +- .../image/cropvolume/tests/main.nf.test | 12 +++++------ .../image/cropvolume/tests/nextflow.config | 2 +- .../cropvolume/tests/nextflow_bbox.config | 2 +- .../nf-neuro/image/cropvolume/tests/tags.yml | 4 ++-- subworkflows/nf-neuro/preproc_dwi/main.nf | 8 ++++---- subworkflows/nf-neuro/preproc_dwi/meta.yml | 2 +- .../nf-neuro/preproc_dwi/tests/main.nf.test | 2 +- .../preproc_dwi/tests/nextflow.config | 2 +- subworkflows/nf-neuro/preproc_t1/main.nf | 20 +++++++++---------- subworkflows/nf-neuro/preproc_t1/meta.yml | 2 +- .../nf-neuro/preproc_t1/tests/main.nf.test | 2 +- .../nf-neuro/preproc_t1/tests/nextflow.config | 2 +- .../preproc_t1/tests/nextflow_synthbet.config | 2 +- 16 files changed, 34 insertions(+), 34 deletions(-) diff --git a/modules/nf-neuro/image/cropvolume/environment.yml b/modules/nf-neuro/image/cropvolume/environment.yml index 3adeaf1e..670802a8 100644 --- a/modules/nf-neuro/image/cropvolume/environment.yml +++ b/modules/nf-neuro/image/cropvolume/environment.yml @@ -1,3 +1,3 @@ channels: [] dependencies: [] -name: betcrop_cropvolume +name: image_cropvolume diff --git a/modules/nf-neuro/image/cropvolume/main.nf b/modules/nf-neuro/image/cropvolume/main.nf index e8f47015..08c5d388 100755 --- a/modules/nf-neuro/image/cropvolume/main.nf +++ b/modules/nf-neuro/image/cropvolume/main.nf @@ -1,5 +1,5 @@ -process BETCROP_CROPVOLUME { +process IMAGE_CROPVOLUME { tag "$meta.id" label 'process_single' diff --git a/modules/nf-neuro/image/cropvolume/meta.yml b/modules/nf-neuro/image/cropvolume/meta.yml index e981e340..df13e950 100755 --- a/modules/nf-neuro/image/cropvolume/meta.yml +++ b/modules/nf-neuro/image/cropvolume/meta.yml @@ -1,6 +1,6 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/scilus/nf-neuro/main/modules/meta-schema.json -name: "betcrop_cropvolume" +name: "image_cropvolume" description: Crop empty planes around the data in a volume keywords: - nifti diff --git a/modules/nf-neuro/image/cropvolume/tests/main.nf.test b/modules/nf-neuro/image/cropvolume/tests/main.nf.test index 06333238..af2c9486 100644 --- a/modules/nf-neuro/image/cropvolume/tests/main.nf.test +++ b/modules/nf-neuro/image/cropvolume/tests/main.nf.test @@ -1,14 +1,14 @@ nextflow_process { - name "Test Process BETCROP_CROPVOLUME" + name "Test Process IMAGE_CROPVOLUME" script "../main.nf" - process "BETCROP_CROPVOLUME" + process "IMAGE_CROPVOLUME" config "./nextflow.config" tag "modules" tag "modules_nfcore" - tag "betcrop" - tag "betcrop/cropvolume" + tag "image" + tag "image/cropvolume" tag "subworkflows" tag "subworkflows/load_test_data" @@ -25,7 +25,7 @@ nextflow_process { } } - test("betcrop - cropvolume") { + test("image - cropvolume") { when { process { @@ -50,7 +50,7 @@ nextflow_process { } - test("betcrop - cropvolume - outputbbox") { + test("image - cropvolume - outputbbox") { config "./nextflow_bbox.config" diff --git a/modules/nf-neuro/image/cropvolume/tests/nextflow.config b/modules/nf-neuro/image/cropvolume/tests/nextflow.config index 7a7632ff..3a9e735d 100644 --- a/modules/nf-neuro/image/cropvolume/tests/nextflow.config +++ b/modules/nf-neuro/image/cropvolume/tests/nextflow.config @@ -1,5 +1,5 @@ process { - withName: "BETCROP_CROPVOLUME" { + withName: "IMAGE_CROPVOLUME" { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } } } diff --git a/modules/nf-neuro/image/cropvolume/tests/nextflow_bbox.config b/modules/nf-neuro/image/cropvolume/tests/nextflow_bbox.config index c998553c..6055585a 100644 --- a/modules/nf-neuro/image/cropvolume/tests/nextflow_bbox.config +++ b/modules/nf-neuro/image/cropvolume/tests/nextflow_bbox.config @@ -1,5 +1,5 @@ process { - withName: "BETCROP_CROPVOLUME" { + withName: "IMAGE_CROPVOLUME" { ext.output_bbox = true publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } } diff --git a/modules/nf-neuro/image/cropvolume/tests/tags.yml b/modules/nf-neuro/image/cropvolume/tests/tags.yml index d6802302..eeae1b2c 100644 --- a/modules/nf-neuro/image/cropvolume/tests/tags.yml +++ b/modules/nf-neuro/image/cropvolume/tests/tags.yml @@ -1,2 +1,2 @@ -betcrop/cropvolume: - - "modules/nf-neuro/betcrop/cropvolume/**" +image/cropvolume: + - "modules/nf-neuro/image/cropvolume/**" diff --git a/subworkflows/nf-neuro/preproc_dwi/main.nf b/subworkflows/nf-neuro/preproc_dwi/main.nf index f16e2a36..c2ee7348 100644 --- a/subworkflows/nf-neuro/preproc_dwi/main.nf +++ b/subworkflows/nf-neuro/preproc_dwi/main.nf @@ -1,7 +1,7 @@ include { DENOISING_MPPCA as DENOISE_DWI } from '../../../modules/nf-neuro/denoising/mppca/main' include { DENOISING_MPPCA as DENOISE_REVDWI } from '../../../modules/nf-neuro/denoising/mppca/main' include { BETCROP_FSLBETCROP } from '../../../modules/nf-neuro/betcrop/fslbetcrop/main' -include { BETCROP_CROPVOLUME } from '../../../modules/nf-neuro/betcrop/cropvolume/main' +include { IMAGE_CROPVOLUME } from '../../../modules/nf-neuro/image/cropvolume/main' include { PREPROC_N4 as N4_DWI } from '../../../modules/nf-neuro/preproc/n4/main' include { PREPROC_NORMALIZE as NORMALIZE_DWI } from '../../../modules/nf-neuro/preproc/normalize/main' include { IMAGE_RESAMPLE as RESAMPLE_DWI } from '../../../modules/nf-neuro/image/resample/main' @@ -78,12 +78,12 @@ workflow PREPROC_DWI { ch_crop_b0 = TOPUP_EDDY.out.b0 .join(BETCROP_FSLBETCROP.out.bbox) - BETCROP_CROPVOLUME ( ch_crop_b0 ) - ch_versions = ch_versions.mix(BETCROP_CROPVOLUME.out.versions.first()) + IMAGE_CROPVOLUME ( ch_crop_b0 ) + ch_versions = ch_versions.mix(IMAGE_CROPVOLUME.out.versions.first()) // ** N4 DWI ** // ch_N4 = BETCROP_FSLBETCROP.out.image - .join(BETCROP_CROPVOLUME.out.image) + .join(IMAGE_CROPVOLUME.out.image) .join(BETCROP_FSLBETCROP.out.mask) N4_DWI ( ch_N4 ) diff --git a/subworkflows/nf-neuro/preproc_dwi/meta.yml b/subworkflows/nf-neuro/preproc_dwi/meta.yml index 705b64e9..6cd12eae 100644 --- a/subworkflows/nf-neuro/preproc_dwi/meta.yml +++ b/subworkflows/nf-neuro/preproc_dwi/meta.yml @@ -45,7 +45,7 @@ keywords: - Normalization - Resampling components: - - betcrop/cropvolume + - image/cropvolume - betcrop/fslbetcrop - denoising/mppca - image/resample diff --git a/subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test b/subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test index 9f8693b3..b3dbc324 100644 --- a/subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test +++ b/subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test @@ -9,7 +9,7 @@ nextflow_workflow { tag "subworkflows_nfcore" tag "subworkflows/preproc_dwi" tag "subworkflows/topup_eddy" - tag "betcrop/cropvolume" + tag "image/cropvolume" tag "betcrop/fslbetcrop" tag "denoising/mppca" tag "image/resample" diff --git a/subworkflows/nf-neuro/preproc_dwi/tests/nextflow.config b/subworkflows/nf-neuro/preproc_dwi/tests/nextflow.config index 4bf578f2..95e0160a 100644 --- a/subworkflows/nf-neuro/preproc_dwi/tests/nextflow.config +++ b/subworkflows/nf-neuro/preproc_dwi/tests/nextflow.config @@ -41,7 +41,7 @@ process { ext.voxel_size = 1 ext.interp = "lin" } - withName: "BETCROP_CROPVOLUME" { + withName: "IMAGE_CROPVOLUME" { ext.output_bbox = false } diff --git a/subworkflows/nf-neuro/preproc_t1/main.nf b/subworkflows/nf-neuro/preproc_t1/main.nf index b923495e..27b51347 100644 --- a/subworkflows/nf-neuro/preproc_t1/main.nf +++ b/subworkflows/nf-neuro/preproc_t1/main.nf @@ -4,8 +4,8 @@ include { PREPROC_N4 } from '../../../modules/nf-neuro/preproc/n4/main' include { IMAGE_RESAMPLE } from '../../../modules/nf-neuro/image/resample/main' include { BETCROP_ANTSBET } from '../../../modules/nf-neuro/betcrop/antsbet/main' include { BETCROP_SYNTHBET} from '../../../modules/nf-neuro/betcrop/synthbet/main' -include { BETCROP_CROPVOLUME as BETCROP_CROPVOLUME_T1 } from '../../../modules/nf-neuro/betcrop/cropvolume/main' -include { BETCROP_CROPVOLUME as BETCROP_CROPVOLUME_MASK } from '../../../modules/nf-neuro/betcrop/cropvolume/main' +include { IMAGE_CROPVOLUME as IMAGE_CROPVOLUME_T1 } from '../../../modules/nf-neuro/image/cropvolume/main' +include { IMAGE_CROPVOLUME as IMAGE_CROPVOLUME_MASK } from '../../../modules/nf-neuro/image/cropvolume/main' params.run_synthbet = false @@ -104,24 +104,24 @@ workflow PREPROC_T1 { ch_crop = image_bet .map{ it + [[]] } - BETCROP_CROPVOLUME_T1 ( ch_crop ) - ch_versions = ch_versions.mix(BETCROP_CROPVOLUME_T1.out.versions.first()) + IMAGE_CROPVOLUME_T1 ( ch_crop ) + ch_versions = ch_versions.mix(IMAGE_CROPVOLUME_T1.out.versions.first()) // ** Crop mask ** // ch_crop_mask = mask_bet - .join(BETCROP_CROPVOLUME_T1.out.bounding_box) + .join(IMAGE_CROPVOLUME_T1.out.bounding_box) - BETCROP_CROPVOLUME_MASK ( ch_crop_mask ) - ch_versions = ch_versions.mix(BETCROP_CROPVOLUME_MASK.out.versions.first()) + IMAGE_CROPVOLUME_MASK ( ch_crop_mask ) + ch_versions = ch_versions.mix(IMAGE_CROPVOLUME_MASK.out.versions.first()) emit: - t1_final = BETCROP_CROPVOLUME_T1.out.image // channel: [ val(meta), t1-preprocessed ] - mask_final = BETCROP_CROPVOLUME_MASK.out.image // channel: [ val(meta), t1-mask ] + t1_final = IMAGE_CROPVOLUME_T1.out.image // channel: [ val(meta), t1-preprocessed ] + mask_final = IMAGE_CROPVOLUME_MASK.out.image // channel: [ val(meta), t1-mask ] image_nlmeans = DENOISING_NLMEANS.out.image // channel: [ val(meta), t1-after-denoise ] image_N4 = PREPROC_N4.out.image // channel: [ val(meta), t1-after-unbias ] image_resample = IMAGE_RESAMPLE.out.image // channel: [ val(meta), t1-after-resample ] image_bet = image_bet // channel: [ val(meta), t1-after-bet ] mask_bet = mask_bet // channel: [ val(meta), intermediary-mask ] - crop_box = BETCROP_CROPVOLUME_T1.out.bounding_box // channel: [ val(meta), bounding-box ] + crop_box = IMAGE_CROPVOLUME_T1.out.bounding_box // channel: [ val(meta), bounding-box ] versions = ch_versions // channel: [ versions.yml ] } diff --git a/subworkflows/nf-neuro/preproc_t1/meta.yml b/subworkflows/nf-neuro/preproc_t1/meta.yml index c06f6f1f..e736187d 100644 --- a/subworkflows/nf-neuro/preproc_t1/meta.yml +++ b/subworkflows/nf-neuro/preproc_t1/meta.yml @@ -45,7 +45,7 @@ components: - image/resample - betcrop/antsbet - betcrop/synthbet - - betcrop/cropvolume + - image/cropvolume input: - ch_image: diff --git a/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test b/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test index 44744117..d5701712 100644 --- a/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test +++ b/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test @@ -13,7 +13,7 @@ nextflow_workflow { tag "image/resample" tag "betcrop/antsbet" tag "betcrop/synthbet" - tag "betcrop/cropvolume" + tag "image/cropvolume" tag "load_test_data" diff --git a/subworkflows/nf-neuro/preproc_t1/tests/nextflow.config b/subworkflows/nf-neuro/preproc_t1/tests/nextflow.config index 0cf9bdfd..cd10f79e 100644 --- a/subworkflows/nf-neuro/preproc_t1/tests/nextflow.config +++ b/subworkflows/nf-neuro/preproc_t1/tests/nextflow.config @@ -4,7 +4,7 @@ process { ext.voxel_size = 1 ext.interp = "lin" } - withName: "BETCROP_CROPVOLUME_T1" { + withName: "IMAGE_CROPVOLUME_T1" { ext.output_bbox = true ext.first_suffix = "t1" } diff --git a/subworkflows/nf-neuro/preproc_t1/tests/nextflow_synthbet.config b/subworkflows/nf-neuro/preproc_t1/tests/nextflow_synthbet.config index ce65c778..081d4805 100644 --- a/subworkflows/nf-neuro/preproc_t1/tests/nextflow_synthbet.config +++ b/subworkflows/nf-neuro/preproc_t1/tests/nextflow_synthbet.config @@ -4,7 +4,7 @@ process { ext.voxel_size = 1 ext.interp = "lin" } - withName: "BETCROP_CROPVOLUME_T1" { + withName: "IMAGE_CROPVOLUME_T1" { ext.output_bbox = true ext.first_suffix = "t1" } From 3e2e971f5bdaafcd5f72cb9c69f9d0b2a6f20de3 Mon Sep 17 00:00:00 2001 From: medde Date: Thu, 12 Dec 2024 19:12:57 +0000 Subject: [PATCH 4/8] add test.snap module --- .../image/cropvolume/tests/main.nf.test.snap | 52 +++++++++---------- 1 file changed, 26 insertions(+), 26 deletions(-) diff --git a/modules/nf-neuro/image/cropvolume/tests/main.nf.test.snap b/modules/nf-neuro/image/cropvolume/tests/main.nf.test.snap index ec0dfa70..b7c47661 100644 --- a/modules/nf-neuro/image/cropvolume/tests/main.nf.test.snap +++ b/modules/nf-neuro/image/cropvolume/tests/main.nf.test.snap @@ -1,5 +1,5 @@ { - "betcrop - cropvolume - outputbbox": { + "image - cropvolume": { "content": [ { "0": [ @@ -12,25 +12,13 @@ ] ], "1": [ - [ - { - "id": "test", - "single_end": false - }, - "test_cropped_bbox.pkl:md5,d6a03b61669b07683e8c4b21a613f16c" - ] + ], "2": [ - "versions.yml:md5,3b089d55a1116feffa69d739ced1d99f" + "versions.yml:md5,c9f9039fc9103e716e831016a61807f9" ], "bounding_box": [ - [ - { - "id": "test", - "single_end": false - }, - "test_cropped_bbox.pkl:md5,d6a03b61669b07683e8c4b21a613f16c" - ] + ], "image": [ [ @@ -42,17 +30,17 @@ ] ], "versions": [ - "versions.yml:md5,3b089d55a1116feffa69d739ced1d99f" + "versions.yml:md5,c9f9039fc9103e716e831016a61807f9" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.10.0" }, - "timestamp": "2024-10-28T19:30:09.320626173" + "timestamp": "2024-12-12T18:59:41.317523464" }, - "betcrop - cropvolume": { + "image - cropvolume - outputbbox": { "content": [ { "0": [ @@ -65,13 +53,25 @@ ] ], "1": [ - + [ + { + "id": "test", + "single_end": false + }, + "test_cropped_bbox.pkl:md5,d6a03b61669b07683e8c4b21a613f16c" + ] ], "2": [ - "versions.yml:md5,3b089d55a1116feffa69d739ced1d99f" + "versions.yml:md5,c9f9039fc9103e716e831016a61807f9" ], "bounding_box": [ - + [ + { + "id": "test", + "single_end": false + }, + "test_cropped_bbox.pkl:md5,d6a03b61669b07683e8c4b21a613f16c" + ] ], "image": [ [ @@ -83,14 +83,14 @@ ] ], "versions": [ - "versions.yml:md5,3b089d55a1116feffa69d739ced1d99f" + "versions.yml:md5,c9f9039fc9103e716e831016a61807f9" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.10.0" }, - "timestamp": "2024-10-28T19:30:00.033087617" + "timestamp": "2024-12-12T18:59:50.080977383" } } \ No newline at end of file From 2d8273c38941b5c8b5ab19955539a24f9a2ef28b Mon Sep 17 00:00:00 2001 From: AlexVCaron Date: Wed, 15 Jan 2025 16:45:47 +0000 Subject: [PATCH 5/8] fix preproc_t1 versions snapshot --- .../nf-neuro/preproc_t1/tests/main.nf.test.snap | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) 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 7f595ab8..0935d472 100644 --- a/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap +++ b/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap @@ -19,10 +19,10 @@ "test_t1_cropped.nii.gz:md5:header,efab188f3700b5b29d4b4ef99cec1295,data,8a93b9d76ead7dae4af4792b9cf70479", [ "versions.yml:md5,318cabe934be45528a25f52083d9c90d", - "versions.yml:md5,37229cd5cee6f6788fbc9083d6618c61", - "versions.yml:md5,657fbb224f260392e573b8511c4b798d", "versions.yml:md5,b979132991d8f72a3585465533bd5730", "versions.yml:md5,bdd934b4b8456060c36d6d97e4f30740", + "versions.yml:md5,be3dbb0ac2589ad263d583018f339102", + "versions.yml:md5,bf4dd58c38dd4863ebfb9e78a94c3a20", "versions.yml:md5,ea32c30f5320f720b2f5dc32ac2535ea" ] ], @@ -44,10 +44,10 @@ "test_t1_cropped.nii.gz", [ "versions.yml:md5,19aaa24cf046e49a4ad4ce5d507ea8aa", - "versions.yml:md5,37229cd5cee6f6788fbc9083d6618c61", - "versions.yml:md5,657fbb224f260392e573b8511c4b798d", "versions.yml:md5,b979132991d8f72a3585465533bd5730", "versions.yml:md5,bdd934b4b8456060c36d6d97e4f30740", + "versions.yml:md5,be3dbb0ac2589ad263d583018f339102", + "versions.yml:md5,bf4dd58c38dd4863ebfb9e78a94c3a20", "versions.yml:md5,ea32c30f5320f720b2f5dc32ac2535ea" ] ], @@ -57,4 +57,4 @@ }, "timestamp": "2024-12-04T10:38:12.185789" } -} \ No newline at end of file +} From 454fc2829b333e6d7461994cddc6d8a34f6b33f8 Mon Sep 17 00:00:00 2001 From: AlexVCaron Date: Wed, 15 Jan 2025 16:47:44 +0000 Subject: [PATCH 6/8] fix preproc_dwi versions snapshot --- subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test.snap | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) 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 370fa97f..81b13fe1 100644 --- a/subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test.snap +++ b/subworkflows/nf-neuro/preproc_dwi/tests/main.nf.test.snap @@ -14,7 +14,7 @@ "versions.yml:md5,0280006ceecc575513278292734ffb27", "versions.yml:md5,0494fbf74bc9c16d2b30cb45b3bba66b", "versions.yml:md5,0b8c908e52917b0b706fc9d1b4d6cd24", - "versions.yml:md5,0e680a0c6b56892e1a7ec7f85bb95322", + "versions.yml:md5,10ec368dc91791041043fddf6ea3d5c9", "versions.yml:md5,571265e710ca29198e69be22c0f970d5", "versions.yml:md5,662ea558da42564a0f6140473132bcb4", "versions.yml:md5,7ddf2e98f59b19c9b933670550f26ad7", @@ -51,7 +51,7 @@ "versions.yml:md5,0280006ceecc575513278292734ffb27", "versions.yml:md5,0494fbf74bc9c16d2b30cb45b3bba66b", "versions.yml:md5,0b8c908e52917b0b706fc9d1b4d6cd24", - "versions.yml:md5,0e680a0c6b56892e1a7ec7f85bb95322", + "versions.yml:md5,10ec368dc91791041043fddf6ea3d5c9", "versions.yml:md5,571265e710ca29198e69be22c0f970d5", "versions.yml:md5,7ddf2e98f59b19c9b933670550f26ad7", "versions.yml:md5,c15ba5efd24564dba4710b6da8c4b791", @@ -87,7 +87,7 @@ "versions.yml:md5,0280006ceecc575513278292734ffb27", "versions.yml:md5,0494fbf74bc9c16d2b30cb45b3bba66b", "versions.yml:md5,0b8c908e52917b0b706fc9d1b4d6cd24", - "versions.yml:md5,0e680a0c6b56892e1a7ec7f85bb95322", + "versions.yml:md5,10ec368dc91791041043fddf6ea3d5c9", "versions.yml:md5,571265e710ca29198e69be22c0f970d5", "versions.yml:md5,662ea558da42564a0f6140473132bcb4", "versions.yml:md5,7ddf2e98f59b19c9b933670550f26ad7", @@ -109,4 +109,4 @@ }, "timestamp": "2024-12-12T18:31:26.492075412" } -} \ No newline at end of file +} From 78bbfb3b39bb67ea2573019f65f0f0495e394117 Mon Sep 17 00:00:00 2001 From: AlexVCaron Date: Wed, 15 Jan 2025 17:22:47 +0000 Subject: [PATCH 7/8] fix preproc_t1 quick versions snapshot --- .../preproc_t1/tests/main.nf.test.snap | 32 +++++++++---------- 1 file changed, 16 insertions(+), 16 deletions(-) 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 f2245cd4..88fda3b4 100644 --- a/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap +++ b/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap @@ -12,7 +12,7 @@ ] ], "1": [ - + ], "2": [ [ @@ -51,18 +51,18 @@ ] ], "6": [ - + ], "7": [ - + ], "8": [ - "versions.yml:md5,657fbb224f260392e573b8511c4b798d", "versions.yml:md5,bdd934b4b8456060c36d6d97e4f30740", + "versions.yml:md5,bf4dd58c38dd4863ebfb9e78a94c3a20", "versions.yml:md5,ea32c30f5320f720b2f5dc32ac2535ea" ], "crop_box": [ - + ], "image_N4": [ [ @@ -101,10 +101,10 @@ ] ], "mask_bet": [ - + ], "mask_final": [ - + ], "t1_final": [ [ @@ -116,8 +116,8 @@ ] ], "versions": [ - "versions.yml:md5,657fbb224f260392e573b8511c4b798d", "versions.yml:md5,bdd934b4b8456060c36d6d97e4f30740", + "versions.yml:md5,bf4dd58c38dd4863ebfb9e78a94c3a20", "versions.yml:md5,ea32c30f5320f720b2f5dc32ac2535ea" ] } @@ -174,7 +174,7 @@ ] ], "1": [ - + ], "2": [ [ @@ -213,16 +213,16 @@ ] ], "6": [ - + ], "7": [ - + ], "8": [ - + ], "crop_box": [ - + ], "image_N4": [ [ @@ -261,10 +261,10 @@ ] ], "mask_bet": [ - + ], "mask_final": [ - + ], "t1_final": [ [ @@ -276,7 +276,7 @@ ] ], "versions": [ - + ] } ], From 64d5fb0a1b75c22160b42f02e2e43501ad064542 Mon Sep 17 00:00:00 2001 From: AlexVCaron Date: Wed, 15 Jan 2025 18:15:01 +0000 Subject: [PATCH 8/8] another update after merge --- subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 509625fa..da31b7df 100644 --- a/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap +++ b/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap @@ -297,11 +297,11 @@ "test_cropped.nii.gz", "test_t1_cropped.nii.gz", [ - "versions.yml:md5,19aaa24cf046e49a4ad4ce5d507ea8aa", "versions.yml:md5,b979132991d8f72a3585465533bd5730", "versions.yml:md5,bdd934b4b8456060c36d6d97e4f30740", "versions.yml:md5,be3dbb0ac2589ad263d583018f339102", "versions.yml:md5,bf4dd58c38dd4863ebfb9e78a94c3a20", + "versions.yml:md5,da278daafbe3afa8454021e2716dd205", "versions.yml:md5,ea32c30f5320f720b2f5dc32ac2535ea" ] ],