From 82ae6d95b34b9c539781c03a43e98d07941ec15f Mon Sep 17 00:00:00 2001 From: arnaudbore Date: Wed, 11 Jun 2025 19:46:27 +0000 Subject: [PATCH 1/5] first commit trying to import eicab --- .../nf-neuro/vascular/eicab/environment.yml | 4 + modules/nf-neuro/vascular/eicab/main.nf | 43 + modules/nf-neuro/vascular/eicab/meta.yml | 53 + .../vascular/eicab/tests/main.nf.test | 31 + .../nf-neuro/vascular/eicab/tests/tags.yml | 2 + poetry.lock | 1661 +++++++++-------- 6 files changed, 991 insertions(+), 803 deletions(-) create mode 100644 modules/nf-neuro/vascular/eicab/environment.yml create mode 100644 modules/nf-neuro/vascular/eicab/main.nf create mode 100644 modules/nf-neuro/vascular/eicab/meta.yml create mode 100644 modules/nf-neuro/vascular/eicab/tests/main.nf.test create mode 100644 modules/nf-neuro/vascular/eicab/tests/tags.yml diff --git a/modules/nf-neuro/vascular/eicab/environment.yml b/modules/nf-neuro/vascular/eicab/environment.yml new file mode 100644 index 00000000..03f2883e --- /dev/null +++ b/modules/nf-neuro/vascular/eicab/environment.yml @@ -0,0 +1,4 @@ +channels: [] +dependencies: [] +name: vascular_eicab + diff --git a/modules/nf-neuro/vascular/eicab/main.nf b/modules/nf-neuro/vascular/eicab/main.nf new file mode 100644 index 00000000..f882a42b --- /dev/null +++ b/modules/nf-neuro/vascular/eicab/main.nf @@ -0,0 +1,43 @@ + +process VASCULAR_EICAB { + tag "$meta.id" + label 'process_medium' + + container "${ 'felixdumais1/eicab:v1.0.1' }" + + input: + tuple val(meta), path(in_tof) + + output: + tuple val(meta), path("*eicab/"), emit: eicabdirectory + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + def out_folder = task.ext.out_folder ?: "${prefix}_eicab" + def resolution = task.ext.resolution ?: "0.625" + """ + /vessel_segmentation_snaillab/eICAB.sh -t $in_tof \ + -o $out_folder \ + -r $resolution + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2) + END_VERSIONS + """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + mkdir -p ${prefix}_eicab/ + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2) + END_VERSIONS + """ +} diff --git a/modules/nf-neuro/vascular/eicab/meta.yml b/modules/nf-neuro/vascular/eicab/meta.yml new file mode 100644 index 00000000..c8e45cb7 --- /dev/null +++ b/modules/nf-neuro/vascular/eicab/meta.yml @@ -0,0 +1,53 @@ +--- +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: "vascular_eicab" +description: "eICAB - A novel deep learning pipeline for Circle of Willis multiclass segmentation and analysis" +keywords: + - angiography + - segmentation + - labelling + - vascular +tools: + - "vascular": + homepage: "https://gitlab.com/FelixDumais/vessel_segmentation_snaillab/" + description: "Automated segmentation and labeling of the main intracranial arteries on MR angiography images" + tool_dev_url: "https://gitlab.com/FelixDumais/vessel_segmentation_snaillab/" + doi: "10.1016/j.neuroimage.2022.119425" + +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'test', single_end:false ]` + mandatory: true + + - in_tof: + type: file + description: ToF MRA image + pattern: "*.{nii/nii.gz}" + mandatory: true + +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. `[ id:'sample1', single_end:false ]` + + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" + + - eicabdirectory: + type: directory + description: Sorted BAM/CRAM/SAM file + pattern: "*.{bam,cram,sam}" + +authors: + - "@arnaudbore" +maintainers: + - "@arnaudbore" +references: + - "eICAB: A novel deep learning pipeline for Circle of Willis multiclass segmentation and analysis" diff --git a/modules/nf-neuro/vascular/eicab/tests/main.nf.test b/modules/nf-neuro/vascular/eicab/tests/main.nf.test new file mode 100644 index 00000000..8e5f9f1e --- /dev/null +++ b/modules/nf-neuro/vascular/eicab/tests/main.nf.test @@ -0,0 +1,31 @@ +nextflow_process { + + name "Test Process VASCULAR_EICAB" + script "../main.nf" + process "VASCULAR_EICAB" + + tag "modules" + tag "modules_nfcore" + tag "vascular" + tag "vascular/eicab" + + test("segmentation - fastsurfer") { + when { + process { + """ + input[0] = [ + [ id:'test', file("/workspaces/nf-neuro/data/sub-OAS30001_ses-d2430_acq-TOF_angio_resampled.nii.gz") ] + ] + """ + } + } + then { + assertAll( + { assert process.success }, + { assert snapshot( + file(process.out.eicabdirectory.get(0).get(1)).name, + process.out.versions).match()} + ) + } + } +} diff --git a/modules/nf-neuro/vascular/eicab/tests/tags.yml b/modules/nf-neuro/vascular/eicab/tests/tags.yml new file mode 100644 index 00000000..1c910b32 --- /dev/null +++ b/modules/nf-neuro/vascular/eicab/tests/tags.yml @@ -0,0 +1,2 @@ +vascular/eicab: + - 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'process_medium' container "${ 'felixdumais1/eicab:v1.0.1' }" + containerOptions { + (workflow.containerEngine == 'docker') ? '--entrypoint ""' : '' + } input: tuple val(meta), path(in_tof) @@ -26,7 +29,7 @@ process VASCULAR_EICAB { cat <<-END_VERSIONS > versions.yml "${task.process}": - scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2) + vessel-segmentation: \$(pip list | grep vessel-segmentation | tr -s ' ' | cut -d' ' -f2) END_VERSIONS """ @@ -37,7 +40,7 @@ process VASCULAR_EICAB { cat <<-END_VERSIONS > versions.yml "${task.process}": - scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2) + vessel-segmentation: \$(pip list | grep vessel-segmentation | tr -s ' ' | cut -d' ' -f2) END_VERSIONS """ } From 8c736090165c1292dca4445d0956beb09be2f45b Mon Sep 17 00:00:00 2001 From: arnaudbore Date: Wed, 11 Jun 2025 20:07:33 +0000 Subject: [PATCH 3/5] fix patern meta --- modules/nf-neuro/vascular/eicab/meta.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-neuro/vascular/eicab/meta.yml b/modules/nf-neuro/vascular/eicab/meta.yml index c8e45cb7..8fe76b5f 100644 --- a/modules/nf-neuro/vascular/eicab/meta.yml +++ b/modules/nf-neuro/vascular/eicab/meta.yml @@ -43,7 +43,7 @@ output: - eicabdirectory: type: directory description: Sorted BAM/CRAM/SAM file - pattern: "*.{bam,cram,sam}" + pattern: "*_eicab/" authors: - "@arnaudbore" From 9f9c939ff00dfe8ffee94eea79a41d82b0140259 Mon Sep 17 00:00:00 2001 From: arnaudbore Date: Wed, 11 Jun 2025 20:32:25 +0000 Subject: [PATCH 4/5] fix typo --- modules/nf-neuro/vascular/eicab/tests/main.nf.test | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-neuro/vascular/eicab/tests/main.nf.test b/modules/nf-neuro/vascular/eicab/tests/main.nf.test index 8e5f9f1e..4cb20e1d 100644 --- a/modules/nf-neuro/vascular/eicab/tests/main.nf.test +++ b/modules/nf-neuro/vascular/eicab/tests/main.nf.test @@ -9,7 +9,7 @@ nextflow_process { tag "vascular" tag "vascular/eicab" - test("segmentation - fastsurfer") { + test("segmentation - eicab") { when { process { """ From d88a8095b5104ee3bd3511d1dd20a67032efab38 Mon Sep 17 00:00:00 2001 From: arnaudbore Date: Thu, 12 Jun 2025 03:05:11 +0000 Subject: [PATCH 5/5] fix local test - working prototype --- modules/nf-neuro/vascular/eicab/main.nf | 5 +++-- modules/nf-neuro/vascular/eicab/meta.yml | 12 ++++++++++-- .../nf-neuro/vascular/eicab/tests/main.nf.test | 4 +++- .../vascular/eicab/tests/main.nf.test.snap | 16 ++++++++++++++++ 4 files changed, 32 insertions(+), 5 deletions(-) create mode 100644 modules/nf-neuro/vascular/eicab/tests/main.nf.test.snap diff --git a/modules/nf-neuro/vascular/eicab/main.nf b/modules/nf-neuro/vascular/eicab/main.nf index 315ab0e9..f50b7c1c 100644 --- a/modules/nf-neuro/vascular/eicab/main.nf +++ b/modules/nf-neuro/vascular/eicab/main.nf @@ -12,8 +12,9 @@ process VASCULAR_EICAB { tuple val(meta), path(in_tof) output: - tuple val(meta), path("*eicab/"), emit: eicabdirectory - path "versions.yml" , emit: versions + tuple val(meta), path("*_eicab") , emit: eicabdirectory + tuple val(meta), path("*_eicab/*_eICAB_CW.nii.gz"), emit: eicabcw + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when diff --git a/modules/nf-neuro/vascular/eicab/meta.yml b/modules/nf-neuro/vascular/eicab/meta.yml index 8fe76b5f..d440c4b6 100644 --- a/modules/nf-neuro/vascular/eicab/meta.yml +++ b/modules/nf-neuro/vascular/eicab/meta.yml @@ -1,7 +1,10 @@ --- # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: "vascular_eicab" -description: "eICAB - A novel deep learning pipeline for Circle of Willis multiclass segmentation and analysis" +description: | + eICAB automatically segments and labels the Internal Carotid Arteries (ICA), Basilar Artery (BA), Anterior Communicating + Artery (AComm), Anterior Cerebral Arteries (ACA), Middle Cerebral Arteries (MCA), Posterior Communicating Arteries ( + PComm), Posterior Cerebral Arteries (PCA), Superior Cerebellar Arteries (SCA) and Anterior Choroidal Arteries (AChA). keywords: - angiography - segmentation @@ -43,7 +46,12 @@ output: - eicabdirectory: type: directory description: Sorted BAM/CRAM/SAM file - pattern: "*_eicab/" + pattern: "*_eicab" + + - eicabcw: + type: file + description: Segmented Circle of Willis (CW) annotated + pattern: "*_eicab_cw.nii.gz" authors: - "@arnaudbore" diff --git a/modules/nf-neuro/vascular/eicab/tests/main.nf.test b/modules/nf-neuro/vascular/eicab/tests/main.nf.test index 4cb20e1d..ff50fe42 100644 --- a/modules/nf-neuro/vascular/eicab/tests/main.nf.test +++ b/modules/nf-neuro/vascular/eicab/tests/main.nf.test @@ -14,7 +14,8 @@ nextflow_process { process { """ input[0] = [ - [ id:'test', file("/workspaces/nf-neuro/data/sub-OAS30001_ses-d2430_acq-TOF_angio_resampled.nii.gz") ] + [ id:'test' ], + [ file("/workspaces/nf-neuro/data/sub-OAS30001_ses-d2430_acq-TOF_angio_resampled.nii.gz") ] ] """ } @@ -24,6 +25,7 @@ nextflow_process { { assert process.success }, { assert snapshot( file(process.out.eicabdirectory.get(0).get(1)).name, + file(process.out.eicabcw.get(0).get(1)).name, process.out.versions).match()} ) } diff --git a/modules/nf-neuro/vascular/eicab/tests/main.nf.test.snap b/modules/nf-neuro/vascular/eicab/tests/main.nf.test.snap new file mode 100644 index 00000000..35462074 --- /dev/null +++ b/modules/nf-neuro/vascular/eicab/tests/main.nf.test.snap @@ -0,0 +1,16 @@ +{ + "segmentation - eicab": { + "content": [ + "test_eicab", + "sub-OAS30001_ses-d2430_acq-TOF_angio_resampled_eICAB_CW.nii.gz", + [ + "versions.yml:md5,6b433c9a3e91fd2a59ac92510ccee4dd" + ] + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "25.04.3" + }, + "timestamp": "2025-06-12T02:51:01.189807007" + } +} \ No newline at end of file