Merge pull request scilus#69 from ThoumyreStanislas/ants_bet_crop

[Module][WIP] Antsbet

modules/nf-scil/betcrop/antsbet/main.nf

@@ -0,0 +1,62 @@
+
+process BETCROP_ANTSBET {
+    tag "$meta.id"
+    label 'process_single'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
+        'scilus/scilus:1.6.0' }"
+
+    input:
+    tuple val(meta), path(t1), path(template), path(tissues_probabilities)
+
+    output:
+    tuple val(meta), path("*t1_bet.nii.gz")     , emit: t1
+    tuple val(meta), path("*t1_bet_mask.nii.gz"), emit: mask
+    path "versions.yml"                         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+    export OMP_NUM_THREADS=1
+    export OPENBLAS_NUM_THREADS=1
+    export ANTS_RANDOM_SEED=1234
+
+    antsBrainExtraction.sh -d 3 -a $t1 -e $template -o bet/ -m $tissues_probabilities -u 0
+    scil_image_math.py convert bet/BrainExtractionMask.nii.gz ${prefix}__t1_bet_mask.nii.gz --data_type uint8
+    mrcalc $t1 ${prefix}__t1_bet_mask.nii.gz -mult ${prefix}__t1_bet.nii.gz -nthreads 1
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: 1.6.0
+        mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
+        ants: 2.4.3
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+        """
+    antsBrainExtraction.sh -h
+    scil_image_math.py -h
+    mrcalc -h
+
+    touch ${prefix}__t1_bet.nii.gz
+    touch ${prefix}__t1_bet_mask.nii.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: 1.6.0
+        mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
+        ants: 2.4.3
+    END_VERSIONS
+    """
+}

modules/nf-scil/betcrop/antsbet/meta.yml

@@ -0,0 +1,65 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "betcrop_antsbet"
+description: Perform Brain extraction using antsBrainExtraction.sh on T1 image.
+keywords:
+  - T1
+  - BET
+  - ants
+tools:
+  - "Scilpy":
+      description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
+      homepage: "https://github.com/scilus/scilpy.git"
+  - "MRtrix3":
+      description: "Toolbox for image processing, analysis and visualisation of dMRI."
+      homepage: "https://mrtrix.readthedocs.io/en/latest/"
+  - "ants":
+      description: "Advanced Normalization Tools."
+      homepage: "https://github.com/ANTsX/ANTs"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - t1:
+      type: file
+      description: Nifti t1 volume to perform BET.
+      pattern: "*.{nii,nii.gz}"
+
+  - template:
+      type: file
+      description: Nifti Anatomical template to perform BET.
+      pattern: "*.{nii,nii.gz}"
+
+  - tissues_probabilities:
+      type: file
+      description: Brain probability mask, with intensity range 1 (definitely brain) to 0 (definitely background).
+      pattern: "*.{nii,nii.gz}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - t1:
+      type: file
+      description: Nifti T1 volume brain-extracted.
+      pattern: "*t1_bet.{nii,nii.gz}"
+
+  - mask:
+      type: file
+      description: T1 mask brain-extracted and cropped.
+      pattern: "*t1_bet_mask.{nii,nii.gz}"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@ThoumyreStanislas"

tests/config/pytest_modules.yml

@@ -1,3 +1,7 @@
+betcrop/antsbet:
+  - modules/nf-scil/betcrop/antsbet/**
+  - tests/modules/nf-scil/betcrop/antsbet/**
+
 betcrop/cropvolume:
   - modules/nf-scil/betcrop/cropvolume/**
   - tests/modules/nf-scil/betcrop/cropvolume/**

tests/config/test_data.config

@@ -18,6 +18,11 @@ params {
                 bval = "${params.test_data_base}/heavy/dwi/dwi.bval"
                 bvec = "${params.test_data_base}/heavy/dwi/dwi.bvec"
             }
+            "antsbet" {
+                t1 = "${params.test_data_base}/heavy/anat/anat_image.nii.gz"
+                template = "${params.test_data_base}/heavy/mni_152/t1_template.nii.gz"
+                map = "${params.test_data_base}/heavy/mni_152/t1_brain_probability_map.nii.gz"
+            }
         }
         "denoising" {
             "nlmeans" {

tests/modules/nf-scil/betcrop/antsbet/main.nf

@@ -0,0 +1,24 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { BETCROP_ANTSBET } from '../../../../../modules/nf-scil/betcrop/antsbet/main.nf'
+include { LOAD_TEST_DATA } from '../../../../../subworkflows/nf-scil/load_test_data/main'
+
+workflow test_betcrop_antsbet {
+
+    input_fetch = Channel.from( [ "antsbet.zip" ] )
+
+    LOAD_TEST_DATA ( input_fetch, "test.test_betcrop_antsbet" )
+
+    input = LOAD_TEST_DATA.out.test_data_directory
+    .map{ test_data_directory -> [
+        [ id:'test', single_end:false ], // meta map
+        file("${test_data_directory}/t1_unaligned.nii.gz"),
+        file("${test_data_directory}/t1_template.nii.gz"),
+        file("${test_data_directory}/t1_brain_probability_map.nii.gz")
+
+    ]}
+
+    BETCROP_ANTSBET ( input )
+}

tests/modules/nf-scil/betcrop/antsbet/nextflow.config

@@ -0,0 +1,6 @@
+process {
+
+    withName: "BETCROP_ANTSBET" {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    }
+}

tests/modules/nf-scil/betcrop/antsbet/test.yml

@@ -0,0 +1,11 @@
+- name: betcrop antsbet test_betcrop_antsbet
+  command: nextflow run ./tests/modules/nf-scil/betcrop/antsbet -entry test_betcrop_antsbet -c ./tests/config/nextflow.config
+  tags:
+    - betcrop/antsbet
+    - betcrop
+  files:
+    - path: output/betcrop/test__t1_bet.nii.gz
+      md5sum: e88c7e63cf220562a97f16c92be0d87b
+    - path: output/betcrop/test__t1_bet_mask.nii.gz
+      md5sum: 846bd8fc8a212dcffcd728a0846a711c
+    - path: output/betcrop/versions.yml