[Module] Freewater module

README.md

@@ -175,7 +175,7 @@ environment.
 ## Contributing to the `nf-scil` project
 
 If you want to propose a new `module` to the repository, follow the guidelines in the
-[module creation](./docs/MODULE.md) documentation. we follow standards closely
+[module creation](./docs/MODULE.md) documentation. We follow standards closely
 aligned with `nf-core`, with some exceptions on process atomicity and how test data is
 handled. Modules that don't abide to them won't be accepted and PR containing them will
 be closed automatically.

docs/MODULE.md

@@ -42,7 +42,7 @@ nf-core modules create \
     --author @scilus \
     --label process_single \
     --meta \
-    <category/tool>
+    <category>/<tool>
 ```
 
 You will still have to interact with the **bioconda** prompt, still select `no`.
@@ -217,7 +217,7 @@ nf-core modules create-test-yml \
     --run-tests \
     --force \
     --no-prompts \
-    <category/tool>
+    <category>/<tool>
 ```
 
 All the test case you defined will be run, watch out for errors ! Once everything runs

modules/nf-scil/reconst/freewater/environment.yml

@@ -0,0 +1,6 @@
+name: "reconst_freewater"
+channels:
+  - Docker
+  - Apptainer
+dependencies:
+  - "scilpy"

modules/nf-scil/reconst/freewater/main.nf

@@ -0,0 +1,78 @@
+
+process RECONST_FREEWATER {
+    tag "$meta.id"
+    label 'process_single'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://scil.usherbrooke.ca/containers/scilus_2.0.0.sif':
+        'scilus/scilus:2.0.0' }"
+
+    input:
+        tuple val(meta), path(dwi), path(bval), path(bvec), path(mask), path(kernels)
+
+    output:
+        tuple val(meta), path("*_dwi_fw_corrected.nii.gz")      , emit: dwi_fw_corrected, optional: true
+        tuple val(meta), path("*_FIT_dir.nii.gz")               , emit: dir, optional: true
+        tuple val(meta), path("*_FIT_FiberVolume.nii.gz")       , emit: fibervolume, optional: true
+        tuple val(meta), path("*_FIT_FW.nii.gz")                , emit: fw, optional: true
+        tuple val(meta), path("*_FIT_nrmse.nii.gz")             , emit: nrmse, optional: true
+        path("kernels")                                         , emit: kernels, optional: true
+        path "versions.yml"                                     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def para_diff = task.ext.para_diff ? "--para_diff " + task.ext.para_diff : ""
+    def perp_diff_min = task.ext.perp_diff_min ? "--perp_diff_min " + task.ext.perp_diff_min : ""
+    def perp_diff_max = task.ext.perp_diff_max ? "--perp_diff_max " + task.ext.perp_diff_max : ""
+    def iso_diff = task.ext.iso_diff ? "--iso_diff " + task.ext.iso_diff : ""
+    def lambda1 = task.ext.lambda1 ? "--lambda1 " + task.ext.lambda1 : ""
+    def lambda2 = task.ext.lambda2 ? "--lambda2 " + task.ext.lambda2 : ""
+    def nb_threads = task.ext.nb_threads ? "--processes " + task.ext.nb_threads : ""
+    def b_thr = task.ext.b_thr ? "--b_thr " + task.ext.b_thr : ""
+    def set_kernels = kernels ? "--load_kernels $kernels" : "--save_kernels kernels/ --compute_only"
+    def set_mask = mask ? "--mask $mask" : ""
+
+    """
+    scil_freewater_maps.py $dwi $bval $bvec $para_diff $perp_diff_min \
+        $perp_diff_max $iso_diff $lambda1 $lambda2 $nb_threads $b_thr \
+        $set_mask $set_kernels
+
+
+    if [ -d "$kernels" ]; then
+        mv results/dwi_fw_corrected.nii.gz ${prefix}__dwi_fw_corrected.nii.gz
+        mv results/FIT_dir.nii.gz ${prefix}__FIT_dir.nii.gz
+        mv results/FIT_FiberVolume.nii.gz ${prefix}__FIT_FiberVolume.nii.gz
+        mv results/FIT_FW.nii.gz ${prefix}__FIT_FW.nii.gz
+        mv results/FIT_nrmse.nii.gz ${prefix}__FIT_nrmse.nii.gz
+
+        rm -rf results
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: 2.0.0
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    scil_freewater_maps.py -h
+    mkdir kernels
+    touch "${prefix}__dwi_fw_corrected.nii.gz"
+    touch "${prefix}__FIT_dir.nii.gz"
+    touch "${prefix}__FIT_FiberVolume.nii.gz"
+    touch "${prefix}__FIT_FW.nii.gz"
+    touch "${prefix}__FIT_nrmse.nii.gz"
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: 2.0.0
+    END_VERSIONS
+    """
+}

modules/nf-scil/reconst/freewater/meta.yml

@@ -0,0 +1,96 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "reconst_freewater"
+description: Run freewater modelling pipeline using AMICO from DWI data.
+keywords:
+  - Diffusion MRI
+  - Freewater
+  - Microstructure modeling
+tools:
+  - "Scilpy":
+      description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
+      homepage: "https://github.com/scilus/scilpy.git"
+  - "Freewater":
+      description: "Free water elimination and mapping from diffusion MRI."
+      doi: "10.1002/mrm.22055"
+  - "AMICO":
+      description: "Accelerated Microstructure Imaging via Convex Optimization."
+      homepage: "https://github.com/daducci/AMICO"
+      doi: "10.1016/j.neuroimage.2014.10.026"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - dwi:
+      type: file
+      description: Nifti DWI file acquired with a freewater compatible protocol (single-shell or multi-shell).
+      pattern: "*.{nii,nii.gz}"
+
+  - bval:
+      type: file
+      description: B-values in FSL format.
+      pattern: "*.bval"
+
+  - bvec:
+      type: file
+      description: B-vectors in FSL format.
+      pattern: "*.bvec"
+
+  - mask:
+      type: file
+      description: Nifti brain mask.
+      pattern: "*mask.{nii,nii.gz}"
+
+  - kernels:
+      type: directory
+      description: Folder containg kernels.
+      pattern: "kernels"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - dwi_fw_corrected:
+      type: file
+      description: Nifti file freewater corrected DWI.
+      pattern: "*__dwi_fw_corrected.{nii,nii.gz}"
+
+  - dir:
+      type: file
+      description: Nifti file main direction.
+      pattern: "*__FIT_dir.{nii,nii.gz}"
+
+  - fibervolume:
+      type: file
+      description: Nifti file for fiber volume.
+      pattern: "*__FIT_fibervolume.{nii,nii.gz}"
+
+  - fw:
+      type: file
+      description: Nifti file for freewater (isotropic volume).
+      pattern: "*__FIT_FW.{nii,nii.gz}"
+
+  - nrmse:
+      type: file
+      description: Nifti file for nrmse.
+      pattern: "*__FIT_nrmse.{nii,nii.gz}"
+
+  - kernels:
+      type: directory
+      description: Folder containing kernels.
+      pattern: "kernels"
+
+  - versions:
+      type: file
+      description: File containing software versions.
+      pattern: "versions.yml"
+
+authors:
+  - "@karanphil"

modules/nf-scil/reconst/freewater/tests/main.nf.test

@@ -0,0 +1,85 @@
+nextflow_process {
+
+    name "Test Process RECONST_FREEWATER"
+    script "../main.nf"
+    process "RECONST_FREEWATER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "reconst"
+    tag "reconst/freewater"
+
+    tag "subworkflows"
+    tag "subworkflows/load_test_data"
+
+    config "./nextflow.config"
+
+    setup {
+            run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
+                script "../../../../../subworkflows/nf-scil/load_test_data/main.nf"
+                process {
+                    """
+                    input[0] = Channel.from( [ "commit_amico.zip" ] )
+                    input[1] = "test.load-test-data"
+                    """
+                }
+            }
+        }
+
+    test("reconst - freewater") {
+
+        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}/dwi.nii.gz", checkIfExists: true),
+                        file("\${test_data_directory}/dwi.bval", checkIfExists: true),
+                        file("\${test_data_directory}/dwi.bvec", checkIfExists: true),
+                        file("\${test_data_directory}/mask.nii.gz", checkIfExists: true),
+                        []
+                    ]
+                 }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("reconst - freewater_no_mask") {
+
+        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}/dwi.nii.gz", checkIfExists: true),
+                        file("\${test_data_directory}/dwi.bval", checkIfExists: true),
+                        file("\${test_data_directory}/dwi.bvec", checkIfExists: true),
+                        [],
+                        []
+                    ]
+                 }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}