create pipeline fiber cup

main.nf

@@ -11,72 +11,79 @@
 
 nextflow.enable.dsl = 2
 
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    GENOME PARAMETER VALUES
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
+params.help = false
 
-// TODO nf-core: Remove this line if you don't need a FASTA file
-//   This is an example of how to use getGenomeAttribute() to fetch parameters
-//   from igenomes.config using `--genome`
-params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta')
+// Importing modules and processes
 
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    VALIDATE & PRINT PARAMETER SUMMARY
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
+include { DENOISING_MPPCA } from "./modules/nf-scil/denoising/mppca/main.nf"
+include { UTILS_EXTRACTB0 } from "../modules/nf-scil/utils/extractb0/main.nf"
+include { BETCROP_FSLBETCROP } from "./modules/nf-scil/betcrop/fslbetcrop/main.nf"
+include { PREPROC_N4 } from "./modules/nf-scil/preproc/n4/main.nf"
+include { RECONST_DTIMETRICS } from "./modules/nf-scil/reconst/dtimetrics/main.nf"
+include { RECONST_FRF } from "./modules/nf-scil/reconst/frf/main.nf"
+include { RECONST_FODF } from "./modules/nf-scil/reconst/fodf/main.nf"
+include { TRACKING_LOCALTRACKING } from "./modules/nf-scil/tracking/localtracking/main.nf"
 
-include { validateParameters; paramsHelp } from 'plugin/nf-validation'
+workflow {
 
-// Print help message if needed
-if (params.help) {
-    def logo = NfcoreTemplate.logo(workflow, params.monochrome_logs)
-    def citation = '\n' + WorkflowMain.citation(workflow) + '\n'
-    def String command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
-    log.info logo + paramsHelp(command) + citation + NfcoreTemplate.dashedLine(params.monochrome_logs)
-    System.exit(0)
-}
+    main:
 
-// Validate input parameters
-if (params.validate_params) {
-    validateParameters()
-}
+        dwi_channel = Channel.fromFilePairs("$input/**/*dwi.nii.gz", size: 1, flat: true)
+            { fetch_id(it.parent, input) }
+        bval_channel = Channel.fromFilePairs("$input/**/*bval", size: 1, flat: true)
+            { fetch_id(it.parent, input) }
+        bvec_channel = Channel.fromFilePairs("$input/**/*bvec", size: 1, flat: true)
+            { fetch_id(it.parent, input) }
 
-WorkflowMain.initialise(workflow, params, log)
+        // ** Denoising ** //
+        DENOISING_MPPCA(dwi_channel)
 
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    NAMED WORKFLOW FOR PIPELINE
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
+        // ** Extract b0 ** //
+        b0_channel = DENOISING_MPPCA.out.dwi
+            .combine(bval_channel)
+            .combine(bvec_channel)
+        UTILS_EXTRACTB0(b0_channel)
 
-include { FIBERCUP } from './workflows/fibercup'
+         // ** Bet ** //
+        bet_channel = DENOISING_MPPCA.out.dwi
+            .combine(bval_channel)
+            .combine(bvec_channel)
+        BETCROP_FSLBETCROP(bet_channel)
 
-//
-// WORKFLOW: Run main nf-core/fibercup analysis pipeline
-//
-workflow NFCORE_FIBERCUP {
-    FIBERCUP ()
-}
+        // ** N4 ** //
+        n4_channel = BETCROP_FSLBETCROP.out.dwi
+            .combine(UTILS_EXTRACTB0.out.b0)
+            .combine(BETCROP_FSLBETCROP.out.mask)
+        PREPROC_N4(n4_channel)
 
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    RUN ALL WORKFLOWS
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
+        // ** DTI ** //
+        dti_channel = PREPROC_N4.out.dwi
+            .combine(bval_channel)
+            .combine(bvec_channel)
+        RECONST_DTIMETRICS(dti_channel)
+
+        // ** FRF ** //
+        frf_channel = PREPROC_N4.out.dwi
+            .combine(bval_channel)
+            .combine(bvec_channel)
+            .combine(b0_mask_channel)
+        RECONST_FRF(frf_channel)
+
+        // ** FODF ** //
+        fodf_channel = PREPROC_N4.out.dwi
+            .combine(bval_channel)
+            .combine(bvec_channel)
+            .combine(b0_mask_channel)
+            .combine(RECONST_DTIMETRICS.out.fa)
+            .combine(RECONST_DTIMETRICS.out.md)
+            .combine(RECONST_FRF.out.frf)
+        RECONST_FODF(fodf_channel)
+
+        // ** Local Tracking ** //
+        tracking_channel = RECONST_FODF.out.fodf
+            .combine(tracking_mask_channel)
+            .combine(seed_channel)
+        TRACKING_LOCALTRACKING(tracking_channel)
 
-//
-// WORKFLOW: Execute a single named workflow for the pipeline
-// See: https://github.com/nf-core/rnaseq/issues/619
-//
-workflow {
-    NFCORE_FIBERCUP ()
 }
 
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    THE END
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/

modules.json

@@ -22,6 +22,57 @@
                     }
                 }
             }
+        },
+        "https://github.com/scilus/nf-scil.git": {
+            "modules": {
+                "nf-scil": {
+                    "betcrop/fslbetcrop": {
+                        "branch": "main",
+                        "git_sha": "701c3dacd90d5129ac11b030dbf461b221dd6937",
+                        "installed_by": ["modules"]
+                    },
+                    "denoising/mppca": {
+                        "branch": "main",
+                        "git_sha": "98796d3551ad5c0ebf6356e375d3850e7cfc64fe",
+                        "installed_by": ["modules"]
+                    },
+                    "denoising/nlmeans": {
+                        "branch": "main",
+                        "git_sha": "c91e5d948830cfc5fc83b984060dd22bf269d81b",
+                        "installed_by": ["modules"]
+                    },
+                    "preproc/n4": {
+                        "branch": "main",
+                        "git_sha": "7eea58371b89dfe254989183fd23262e233d4653",
+                        "installed_by": ["modules"]
+                    },
+                    "reconst/dtimetrics": {
+                        "branch": "main",
+                        "git_sha": "ef9ea4fd26019062173a9bba52ca4914a4944c0c",
+                        "installed_by": ["modules"]
+                    },
+                    "reconst/fodf": {
+                        "branch": "main",
+                        "git_sha": "4c325c5be9a4f8d6a45172d5b6a9fc932c945b0f",
+                        "installed_by": ["modules"]
+                    },
+                    "reconst/frf": {
+                        "branch": "main",
+                        "git_sha": "1c1dda1aae448bc64bc738d13ddcca76ae5448c8",
+                        "installed_by": ["modules"]
+                    },
+                    "tracking/pfttracking": {
+                        "branch": "main",
+                        "git_sha": "0560d8365bdb14d3722aebbd9f3d3be3a70698bb",
+                        "installed_by": ["modules"]
+                    },
+                    "utils/extractb0": {
+                        "branch": "main",
+                        "git_sha": "6b200ce524794bd512c5590bba38c2662dce1e46",
+                        "installed_by": ["modules"]
+                    }
+                }
+            }
         }
     }
 }

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

@@ -0,0 +1,75 @@
+
+process BETCROP_FSLBETCROP {
+    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(dwi), path(bval), path(bvec)
+
+    output:
+        tuple val(meta), path("*dwi_bet_cropped.nii.gz")            , emit: dwi
+        tuple val(meta), path("*dwi_bet_cropped_mask.nii.gz")       , emit: mask
+        tuple val(meta), path("*dwi_boundingBox.pkl")               , emit: bbox
+        path "versions.yml"                                         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def b0_thr = task.ext.b0_thr ? "--b0_thr " + task.ext.b0_thr : ""
+    def bet_dwi_f = task.ext.bet_dwi_f ? "-f " + task.ext.bet_dwi_f : ""
+
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+    export OMP_NUM_THREADS=1
+    export OPENBLAS_NUM_THREADS=1
+
+    scil_extract_b0.py $dwi $bval $bvec ${prefix}__b0.nii.gz --mean \
+        $b0_thr --force_b0_threshold
+    bet ${prefix}__b0.nii.gz ${prefix}__b0_bet.nii.gz -m -R $bet_dwi_f
+    scil_image_math.py convert ${prefix}__b0_bet_mask.nii.gz ${prefix}__b0_bet_mask.nii.gz --data_type uint8 -f
+    mrcalc $dwi ${prefix}__b0_bet_mask.nii.gz -mult ${prefix}__dwi_bet.nii.gz -quiet -nthreads 1
+
+    scil_crop_volume.py $dwi ${prefix}__dwi_bet_cropped.nii.gz -f \
+        --output_bbox ${prefix}__dwi_boundingBox.pkl -f
+    scil_crop_volume.py ${prefix}__b0_bet_mask.nii.gz ${prefix}__dwi_bet_cropped_mask.nii.gz -f\
+        --input_bbox ${prefix}__dwi_boundingBox.pkl -f
+    scil_image_math.py convert ${prefix}__dwi_bet_cropped_mask.nii.gz ${prefix}__dwi_bet_cropped_mask.nii.gz \
+        --data_type uint8 -f
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: 1.6.0
+        mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
+        fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    scil_extract_b0.py -h
+    bet -h
+    scil_image_math.py -h
+    mrcalc -h
+    scil_crop_volume.py -h
+
+    touch ${prefix}__dwi_bet_cropped.nii.gz
+    touch ${prefix}__dwi_bet_cropped_mask.nii.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: 1.6.0
+        mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
+        fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')
+    END_VERSIONS
+    """
+}

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

@@ -0,0 +1,70 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "betcrop_fslbetcrop"
+description: Perform Brain extraction using FSL BET followed by cropping empty planes around the data.
+keywords:
+  - DWI
+  - BET
+  - Crop
+tools:
+  - "FSL":
+      description: "FSL Toolbox and Scilpy Toolbox"
+      homepage: "https://fsl.fmrib.ox.ac.uk/fsl/fslwiki"
+  - "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/"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - dwi:
+      type: file
+      description: Nifti DWI volume to perform BET + crop.
+      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"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+  - dwi:
+      type: file
+      description: Nifti DWI volume brain-extracted and cropped.
+      pattern: "*dwi_bet_cropped.{nii,nii.gz}"
+
+  - mask:
+      type: file
+      description: DWI mask brain-extracted and cropped.
+      pattern: "*dwi_bet_cropped_mask.{nii,nii.gz}"
+
+  - bbox:
+      type: file
+      description: DWI BoundingBox used for cropping. 
+      pattern: "*dwi_boundingBox.pkl"
+
+authors:
+  - "@gagnonanthony"

modules/nf-scil/denoising/mppca/main.nf

@@ -0,0 +1,55 @@
+
+process DENOISING_MPPCA {
+    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(dwi)
+
+    output:
+    tuple val(meta), path("*_dwi_denoised.nii.gz")  , emit: image
+    path "versions.yml"                             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def extent = task.ext.extent ? "-extent " + task.ext.extent : ""
+
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+    export OMP_NUM_THREADS=1
+    export OPENBLAS_NUM_THREADS=1
+
+    dwidenoise $dwi ${prefix}__pre_dwi_denoised.nii.gz $extent -nthreads 1
+    fslmaths ${prefix}__pre_dwi_denoised.nii.gz -thr 0 ${prefix}_dwi_denoised.nii.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
+        fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    dwidenoise -h
+    fslmaths -h
+
+    touch ${prefix}_dwi_denoised.nii.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
+        fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')
+    END_VERSIONS
+    """
+}