diff --git a/main.nf b/main.nf
index b1ad6cd..21781ca 100644
--- a/main.nf
+++ b/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
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-*/
diff --git a/modules.json b/modules.json
index 0c07c6b..c67f10e 100644
--- a/modules.json
+++ b/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"]
+                    }
+                }
+            }
         }
     }
 }
diff --git a/modules/nf-scil/betcrop/fslbetcrop/main.nf b/modules/nf-scil/betcrop/fslbetcrop/main.nf
new file mode 100644
index 0000000..ba25ac9
--- /dev/null
+++ b/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
+    """
+}
diff --git a/modules/nf-scil/betcrop/fslbetcrop/meta.yml b/modules/nf-scil/betcrop/fslbetcrop/meta.yml
new file mode 100644
index 0000000..fe7d76c
--- /dev/null
+++ b/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"
diff --git a/modules/nf-scil/denoising/mppca/main.nf b/modules/nf-scil/denoising/mppca/main.nf
new file mode 100644
index 0000000..c287502
--- /dev/null
+++ b/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
+    """
+}
diff --git a/modules/nf-scil/denoising/mppca/meta.yml b/modules/nf-scil/denoising/mppca/meta.yml
new file mode 100644
index 0000000..d044773
--- /dev/null
+++ b/modules/nf-scil/denoising/mppca/meta.yml
@@ -0,0 +1,49 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "denoising_mppca"
+description: denoise a dataset with the Marchenko-Pastur principal component analysis 
+keywords:
+  - nifti
+  - denoising
+  - mppca
+  - mrtrix
+  - fsl
+tools:
+   - "MRtrix3":
+      description: "Toolbox for image processing, analysis and visualisation of dMRI."
+      homepage: "https://mrtrix.readthedocs.io/en/latest/"
+  - "FSL":
+      description: "FSL Toolbox and Scilpy Toolbox"
+      homepage: "https://fsl.fmrib.ox.ac.uk/fsl/fslwiki"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - dwi:
+      type: file
+      description: Nifti dwi file to denoise
+      pattern: "*.{nii,nii.gz}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+  
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  
+  - image:
+      type: file
+      description: Denoised Nifti image file
+      pattern: "*_dwi_denoised.{nii,nii.gz}"
+
+authors:
+  - "@scilus"
diff --git a/modules/nf-scil/denoising/nlmeans/main.nf b/modules/nf-scil/denoising/nlmeans/main.nf
new file mode 100644
index 0000000..c913d62
--- /dev/null
+++ b/modules/nf-scil/denoising/nlmeans/main.nf
@@ -0,0 +1,51 @@
+
+process DENOISING_NLMEANS {
+    tag "$meta.id"
+    label 'process_single'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
+        'scilus/scilus:1.6.0' }"
+
+    input:
+    tuple val(meta), path(image), path(mask)
+
+    output:
+    tuple val(meta), path("*_denoised.nii.gz")      , emit: image
+    path "versions.yml"                             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args = []
+    if (mask) args += ["--mask $mask"]
+
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+    export OMP_NUM_THREADS=1
+    export OPENBLAS_NUM_THREADS=1
+
+    scil_run_nlmeans.py $image ${prefix}_denoised.nii.gz 1 ${args.join(" ")}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: 1.6.0
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    
+    """
+    scil_run_nlmeans.py -h
+
+    touch ${prefix}_denoised.nii.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: 1.6.0
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-scil/denoising/nlmeans/meta.yml b/modules/nf-scil/denoising/nlmeans/meta.yml
new file mode 100644
index 0000000..050958e
--- /dev/null
+++ b/modules/nf-scil/denoising/nlmeans/meta.yml
@@ -0,0 +1,50 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "denoising_nlmeans"
+description: denoise a dataset with the Non Local Means algorithm
+keywords:
+  - nifti
+  - denoising
+  - nlmeans
+  - scilpy
+tools:
+  - "Scilpy":
+      description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
+      homepage: "https://github.com/scilus/scilpy.git"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - image:
+      type: file
+      description: Nifti image file to denoise
+      pattern: "*.{nii,nii.gz}"
+
+  - mask:
+      type: file
+      description: Nifti image file used to mask the input image
+      pattern: "*.{nii,nii.gz}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+  
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  
+  - image:
+      type: file
+      description: Denoised Nifti image file
+      pattern: "*_denoised.{nii,nii.gz}"
+
+authors:
+  - "@scilus"
diff --git a/modules/nf-scil/preproc/n4/main.nf b/modules/nf-scil/preproc/n4/main.nf
new file mode 100644
index 0000000..7013793
--- /dev/null
+++ b/modules/nf-scil/preproc/n4/main.nf
@@ -0,0 +1,57 @@
+process PREPROC_N4 {
+    tag "$meta.id"
+    label 'process_single'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
+        'scilus/scilus:1.6.0' }"
+
+    input:
+    tuple val(meta), path(dwi), path(b0), path(b0_mask)
+
+    output:
+    tuple val(meta), path("*dwi_n4.nii.gz")     , emit: dwi
+    path "versions.yml"                         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=$task.cpus
+    export OMP_NUM_THREADS=1
+    export OPENBLAS_NUM_THREADS=1
+    export ANTS_RANDOM_SEED=1234
+
+    N4BiasFieldCorrection -i $b0\
+        -o [${prefix}__b0_n4.nii.gz, bias_field_b0.nii.gz]\
+        -c [300x150x75x50, 1e-6] -v 1
+
+    scil_apply_bias_field_on_dwi.py $dwi bias_field_b0.nii.gz\
+        ${prefix}__dwi_n4.nii.gz --mask $b0_mask -f
+
+    cat <<-END_VERSIONS > versions.yml
+        "${task.process}":
+            scilpy: 1.6.0
+            N4BiasFieldCorrection: \$(N4BiasFieldCorrection --version 2>&1 | sed -n 's/ANTs Version: v\\([0-9.]\\+\\)/\\1/p')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    N4BiasFieldCorrection.py -h
+    scil_apply_bias_field_on_dwi -h
+
+    touch ${prefix}_dwi_n4.nii.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: 1.6.0
+            N4BiasFieldCorrection: \$(N4BiasFieldCorrection --version 2>&1 | sed -n 's/ANTs Version: v\\([0-9.]\\+\\)/\\1/p')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-scil/preproc/n4/meta.yml b/modules/nf-scil/preproc/n4/meta.yml
new file mode 100644
index 0000000..ef2cc8b
--- /dev/null
+++ b/modules/nf-scil/preproc/n4/meta.yml
@@ -0,0 +1,54 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "preproc_n4"
+description: Bias field correction using N4
+keywords:
+  - correction
+  - N4
+  - bias field
+tools:
+  - "Scilpy":
+      description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
+      homepage: "https://github.com/scilus/scilpy.git"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+  
+  - dwi:
+      type: file
+      description: Nifti image file to correct
+      pattern: "*.{nii,nii.gz}"
+
+  - b0:
+      type: file
+      description: Nifti image file - b0
+      pattern: "*.{nii,nii.gz}"
+
+  - b0_mask:
+      type: file
+      description: Nifti image file mask
+      pattern: "*.{nii,nii.gz}"        
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+  
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+  - dwi:
+      type: file
+      description: DWI image N4 corrected
+      pattern: "*.{nii,nii.gz}"
+
+authors:
+  - "@arnaudbore"
diff --git a/modules/nf-scil/reconst/dtimetrics/main.nf b/modules/nf-scil/reconst/dtimetrics/main.nf
new file mode 100644
index 0000000..1724f4c
--- /dev/null
+++ b/modules/nf-scil/reconst/dtimetrics/main.nf
@@ -0,0 +1,119 @@
+
+process RECONST_DTIMETRICS {
+    tag "$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), path(b0mask)
+
+    output:
+        tuple val(meta), path("*__ad.nii.gz")                      , emit: ad, optional: true
+        tuple val(meta), path("*__evecs.nii.gz")                   , emit: evecs, optional: true
+        tuple val(meta), path("*__evecs_v1.nii.gz")                , emit: evecs_v1, optional: true
+        tuple val(meta), path("*__evecs_v2.nii.gz")                , emit: evecs_v2, optional: true
+        tuple val(meta), path("*__evecs_v3.nii.gz")                , emit: evecs_v3, optional: true
+        tuple val(meta), path("*__evals.nii.gz")                   , emit: evals, optional: true
+        tuple val(meta), path("*__evals_e1.nii.gz")                , emit: evals_e1, optional: true
+        tuple val(meta), path("*__evals_e2.nii.gz")                , emit: evals_e2, optional: true
+        tuple val(meta), path("*__evals_e3.nii.gz")                , emit: evals_e3, optional: true
+        tuple val(meta), path("*__fa.nii.gz")                      , emit: fa, optional: true
+        tuple val(meta), path("*__ga.nii.gz")                      , emit: ga, optional: true
+        tuple val(meta), path("*__rgb.nii.gz")                     , emit: rgb, optional: true
+        tuple val(meta), path("*__md.nii.gz")                      , emit: md, optional: true
+        tuple val(meta), path("*__mode.nii.gz")                    , emit: mode, optional: true
+        tuple val(meta), path("*__norm.nii.gz")                    , emit: norm, optional: true
+        tuple val(meta), path("*__rd.nii.gz")                      , emit: rd, optional: true
+        tuple val(meta), path("*__tensor.nii.gz")                  , emit: tensor, optional: true
+        tuple val(meta), path("*__nonphysical.nii.gz")             , emit: nonphysical, optional: true
+        tuple val(meta), path("*__pulsation_std_dwi.nii.gz")       , emit: pulsation_std_dwi, optional: true
+        tuple val(meta), path("*__residual.nii.gz")                , emit: residual, optional: true
+        tuple val(meta), path("*__residual_iqr_residuals.npy")     , emit: residual_iqr_residuals, optional: true
+        tuple val(meta), path("*__residual_mean_residuals.npy")    , emit: residual_mean_residuals, optional: true
+        tuple val(meta), path("*__residual_q1_residuals.npy")      , emit: residual_q1_residuals, optional: true
+        tuple val(meta), path("*__residual_q3_residuals.npy")      , emit: residual_q3_residuals, optional: true
+        tuple val(meta), path("*__residual_residuals_stats.png")   , emit: residual_residuals_stats, optional: true
+        tuple val(meta), path("*__residual_std_residuals.npy")     , emit: residual_std_residuals, optional: true
+        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}"
+    def mask =[]
+
+    if (b0mask) mask += ["--mask $b0mask"]
+    if ( task.ext.ad ) args += " --ad ${prefix}__ad.nii.gz"
+    if ( task.ext.evecs ) args += " --evecs ${prefix}__evecs.nii.gz"
+    if ( task.ext.evals ) args += " --evals ${prefix}__evals.nii.gz"
+    if ( task.ext.fa ) args += " --fa ${prefix}__fa.nii.gz"
+    if ( task.ext.ga ) args += " --ga ${prefix}__ga.nii.gz"
+    if ( task.ext.rgb ) args += " --rgb ${prefix}__rgb.nii.gz"
+    if ( task.ext.md ) args += " --md ${prefix}__md.nii.gz"
+    if ( task.ext.mode ) args += " --mode ${prefix}__mode.nii.gz"
+    if ( task.ext.norm ) args += " --norm ${prefix}__norm.nii.gz"
+    if ( task.ext.rd ) args += " --rd ${prefix}__rd.nii.gz"
+    if ( task.ext.tensor ) args += " --tensor ${prefix}__tensor.nii.gz"
+    if ( task.ext.nonphysical ) args += " --non-physical ${prefix}__nonphysical.nii.gz"
+    if ( task.ext.pulsation ) args += " --pulsation ${prefix}__pulsation_std_dwi.nii.gz"
+    if ( task.ext.residual ) args += " --residual ${prefix}__residual.nii.gz"
+
+
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+    export OMP_NUM_THREADS=1
+    export OPENBLAS_NUM_THREADS=1
+
+    scil_compute_dti_metrics.py $dwi $bval $bvec ${mask.join(" ")} --not_all $args -f --force_b0_threshold
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: 1.6.0
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    scil_compute_dti_metrics.py -h
+
+    touch ${prefix}__ad.nii.gz
+    touch ${prefix}__evecs.nii.gz
+    touch ${prefix}__evecs_v1.nii.gz
+    touch ${prefix}__evecs_v2.nii.gz
+    touch ${prefix}__evecs_v3.nii.gz
+    touch ${prefix}__evals.nii.gz
+    touch ${prefix}__evals_e1.nii.gz
+    touch ${prefix}__evals_e2.nii.gz
+    touch ${prefix}__evals_e3.nii.gz
+    touch ${prefix}__fa.nii.gz
+    touch ${prefix}__ga.nii.gz
+    touch ${prefix}__rgb.nii.gz
+    touch ${prefix}__md.nii.gz
+    touch ${prefix}__mode.nii.gz
+    touch ${prefix}__norm.nii.gz
+    touch ${prefix}__rd.nii.gz
+    touch ${prefix}__tensor.nii.gz
+    touch ${prefix}__nonphysical.nii.gz
+    touch ${prefix}__pulsation_std_dwi.nii.gz
+    touch ${prefix}__residual.nii.gz
+    touch ${prefix}__residual_iqr_residuals.npy
+    touch ${prefix}__residual_mean_residuals.npy
+    touch ${prefix}__residual_q1_residuals.npy
+    touch ${prefix}__residual_q3_residuals.npy
+    touch ${prefix}__residual_residuals_stats.png
+    touch ${prefix}__residual_std_residuals.npy
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: 1.6.0
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-scil/reconst/dtimetrics/meta.yml b/modules/nf-scil/reconst/dtimetrics/meta.yml
new file mode 100644
index 0000000..54a2198
--- /dev/null
+++ b/modules/nf-scil/reconst/dtimetrics/meta.yml
@@ -0,0 +1,190 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "reconst_dtimetrics"
+
+description: Script to compute all of the Diffusion Tensor Imaging (DTI) metrics
+keywords:
+  - nifti
+  - DTI
+  - tensor
+  - 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 ]`
+  
+  - dwi:
+      type: file
+      description: Nifti DWI volume used to extract DTI metrics.
+      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"
+
+  - b0mask:
+      type: file
+      description: Nifti b0 volume file used to mask the input image.
+      pattern: "*.{nii,nii.gz}"
+
+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"
+
+  - ad:
+      type: file
+      description: Output filename for the axial diffusivity.
+      pattern: "*__ad.{nii,nii.gz}"
+  
+  - evecs:
+      type: file
+      description: Output filename for the eigenvectors of the tensor.
+      pattern: "*__evecs.{nii,nii.gz}"
+
+  - evecs_v1:
+      type: file
+      description: Output filename for the first eigenvector.
+      pattern: "*__evecs_v1.{nii,nii.gz}"
+
+  - evecs_v2:
+      type: file
+      description: Output filename for the second eigenvector.
+      pattern: "*__evecs_v2.{nii,nii.gz}"
+
+  - evec_v3:
+      type: file
+      description: Output filename for the third eigenvector.
+      pattern: "*__evecs_v3.{nii,nii.gz}"
+
+  - evals:
+      type: file
+      description: Output filename for the eigenvalues of the tensor.
+      pattern: "*__evals.{nii,nii.gz}"
+
+  - evals_e1:
+      type: file
+      description: Output filename for the first eigenvalue.
+      pattern: "*__evals_e1.{nii,nii.gz}"
+
+  - evals_e2:
+      type: file
+      description: Output filename for the second eigenvalue.
+      pattern: "*__evals_e2.{nii,nii.gz}"
+
+  - evals_e3:
+      type: file
+      description: Output filename for the third eigenvalue.
+      pattern: "*__evals_e3.{nii,nii.gz}"
+
+  - fa:
+      type: file
+      description: Output filename for the fractional anisotropy.
+      pattern: "*__fa.{nii,nii.gz}"
+
+  - ga:
+      type: file
+      description: Output filename for the geodesic anisotropy.
+      pattern: "*__ga.{nii,nii.gz}"Cropped Nifti image file
+
+  - rgb:
+      type: file
+      description: Output filename for the colored fractional anisotropy.
+      pattern: "*__rgb.{nii,nii.gz}"
+
+  - md:
+      type: file
+      description: Output filename for the mean diffusivity.
+      pattern: "*__md.{nii,nii.gz}"
+
+  - mode:
+      type: file
+      description: Output filename for the mode.
+      pattern: "*__mode.{nii,nii.gz}"
+
+  - norm:
+      type: file
+      description: Output filename for the tensor norm.
+      pattern: "*__norm.{nii,nii.gz}"
+
+  - rd:
+      type: file
+      description: Output filename for the radial diffusivity.
+      pattern: "*__rd.{nii,nii.gz}"
+
+  - tensor:
+      type: file
+      description: Output filename for the tensor coefficients.
+      pattern: "*__tensor.{nii,nii.gz}"
+
+  - nonphysical:
+      type: file
+      description: Output filename for the voxels with physically implausible 
+                   signals where the mean of b=0 images is below one or more 
+                   diffusion-weighted images.
+      pattern: "*__nonphysical.{nii,nii.gz}"
+
+  - pulsation_std_dwi:
+      type: file
+      description: Standard deviation map across all diffusion-weighted images 
+                   and across b=0 images if more than one is available.Shows 
+                   pulsation and misalignment artifacts.
+      pattern: "*__pulsation_std_dwi.{nii,nii.gz}"
+
+  - residual:
+      type: file
+      description: Output filename for the map of the residual of the tensor fit.
+      pattern: "*__residual.{nii,nii.gz}"
+
+  - residual_iqr_residuals:
+      type: file
+      description: Output filename for the interquartile range of the residual of the tensor fit.
+      pattern: "*__residual_iqr_residuals.npy"
+
+  - residual_mean_residuals:
+      type: file
+      description: Output filename for the mean of the residual of the tensor fit.
+      pattern: "*__residual_mean_residuals.npy"
+
+  - residuall_q1_residuals:
+      type: file
+      description: Output filename for the firt quartile of the residual of the tensor fit.
+      pattern: "*__residual_q1_residuals.npy"
+
+  - residual_q3_residuals:
+      type: file
+      description: Output filename for the third quartile of the residual of the tensor fit.
+      pattern: "*__residual_q3_residuals.npy"
+
+  - residual_residuals_stats:
+      type: file
+      description: Output filename for the all statistics of the residual of the tensor fit.
+      pattern: "*__residual_residuals_stats.png"
+
+  - residual_std_residuals:
+      type: file
+      description: Output filename for the standard deviation of the residual of the tensor fit.
+      pattern: "*__residual_std_residuals.npy"
+
+authors:
+  - "@scilus"
diff --git a/modules/nf-scil/reconst/fodf/main.nf b/modules/nf-scil/reconst/fodf/main.nf
new file mode 100644
index 0000000..a711ad2
--- /dev/null
+++ b/modules/nf-scil/reconst/fodf/main.nf
@@ -0,0 +1,105 @@
+
+process RECONST_FODF {
+    tag "$meta.id"
+    label 'process_single'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
+        'scilus/scilus:1.6.0' }"
+
+    input:
+        tuple val(meta), path(dwi), path(bval), path(bvec), path(b0_mask), path(fa), path(md), path(frf)
+
+    output:
+        tuple val(meta), path("*fodf.nii.gz")           , emit: fodf
+        tuple val(meta), path("*peaks.nii.gz")          , emit: peaks, optional: true
+        tuple val(meta), path("*peak_indices.nii.gz")   , emit: peak_indices, optional: true
+        tuple val(meta), path("*afd_max.nii.gz")        , emit: afd_max, optional: true
+        tuple val(meta), path("*afd_total.nii.gz")      , emit: afd_total, optional: true
+        tuple val(meta), path("*afd_sum.nii.gz")        , emit: afd_sum, optional: true
+        tuple val(meta), path("*nufo.nii.gz")           , emit: nufo, optional: true
+        path "versions.yml"                             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def dwi_shell_tolerance = task.ext.dwi_shell_tolerance ? "--tolerance " + task.ext.dwi_shell_tolerance : ""
+    def fodf_shells = task.ext.fodf_shells ?: "\$(cut -d ' ' --output-delimiter=\$'\\n' -f 1- $bval | awk -F' ' '{v=int(\$1)}{if(v>=$task.ext.min_fodf_shell_value|| v<=$task.ext.b0_thr_extract_b0)print v}' | uniq)"
+    def sh_order = task.ext.sh_order ? "--sh_order " + task.ext.sh_order : ""
+    def sh_basis = task.ext.sh_basis ? "--sh_basis " + task.ext.sh_basis : ""
+    def fa_threshold = task.ext.fa_threshold ? "--fa_t " + task.ext.fa_threshold : ""
+    def md_threshold = task.ext.md_threshold ? "--md_t " + task.ext.md_threshold : ""
+    def relative_threshold = task.ext.relative_threshold ? "--rt " + task.ext.relative_threshold : ""
+    def fodf_metrics_a_factor = task.ext.fodf_metrics_a_factor ? task.ext.fodf_metrics_a_factor : 2.0
+    def processes = task.ext.processes ? "--processes " + task.ext.processes : ""
+
+    if ( task.ext.peaks ) peaks = "--peaks ${prefix}__peaks.nii.gz" else ""
+    if ( task.ext.peak_indices ) peak_indices = "--peak_indices ${prefix}__peak_indices.nii.gz" else ""
+    if ( task.ext.afd_max ) afd_max = "--afd_max ${prefix}__afd_max.nii.gz" else ""
+    if ( task.ext.afd_total ) afd_total = "--afd_total ${prefix}__afd_total.nii.gz" else ""
+    if ( task.ext.afd_sum ) afd_sum = "--afd_sum ${prefix}__afd_sum.nii.gz" else ""
+    if ( task.ext.nufo ) nufo = "--nufo ${prefix}__nufo.nii.gz" else ""
+
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+    export OMP_NUM_THREADS=1
+    export OPENBLAS_NUM_THREADS=1
+
+    scil_extract_dwi_shell.py $dwi $bval $bvec $fodf_shells \
+        dwi_fodf.nii.gz bval_fodf bvec_fodf \
+        $dwi_shell_tolerance -f
+    
+    scil_compute_ssst_fodf.py dwi_fodf.nii.gz bval_fodf bvec_fodf $frf ${prefix}__fodf.nii.gz \
+        $sh_order $sh_basis --force_b0_threshold \
+        --mask $b0_mask $processes
+    
+    scil_compute_fodf_max_in_ventricles.py ${prefix}__fodf.nii.gz $fa $md \
+        --max_value_output ventricles_fodf_max_value.txt $sh_basis \
+        $fa_threshold $md_threshold -f
+
+    a_factor=$fodf_metrics_a_factor
+    v_max=\$(sed -E 's/([+-]?[0-9.]+)[eE]\\+?(-?)([0-9]+)/(\\1*10^\\2\\3)/g' <<<"\$(cat ventricles_fodf_max_value.txt)")
+    a_threshold=\$(echo "scale=10; \${a_factor} * \${v_max}" | bc)
+    if (( \$(echo "\${a_threshold} < 0" | bc -l) )); then
+        a_threshold=0
+    fi
+
+    scil_compute_fodf_metrics.py ${prefix}__fodf.nii.gz \
+        --mask $b0_mask $sh_basis \
+        $peaks $peak_indices \
+        $afd_max $afd_total \
+        $afd_sum $nufo \
+        $relative_threshold --at \${a_threshold}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: 1.6.0
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    scil_extract_dwi_shell.py -h
+    scil_compute_ssst_fodf.py -h
+    scil_compute_fodf_max_in_ventricles.py -h
+    scil_compute_fodf_metrics.py -h
+
+    touch ${prefix}__fodf.nii.gz
+    touch ${prefix}__peaks.nii.gz
+    touch ${prefix}__peak_indices.nii.gz
+    touch ${prefix}__afd_max.nii.gz
+    touch ${prefix}__afd_total.nii.gz
+    touch ${prefix}__afd_sum.nii.gz
+    touch ${prefix}__nufo.nii.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: 1.6.0
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-scil/reconst/fodf/meta.yml b/modules/nf-scil/reconst/fodf/meta.yml
new file mode 100644
index 0000000..fd2366b
--- /dev/null
+++ b/modules/nf-scil/reconst/fodf/meta.yml
@@ -0,0 +1,103 @@
+---
+name: "reconst_fodf"
+description: Perform FODF reconstruction and compute FODF metrics from a dwi volume for a selected number of shells.
+keywords:
+  - FODF
+  - Local Model
+  - Metrics
+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 ]`
+
+  - dwi:
+      type: file
+      description: Nifti DWI volume to reconstruct FODF from.
+      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"
+
+  - b0_mask:
+      type: file
+      description: B0 mask.
+      pattern: "*.{nii,nii.gz}"
+
+  - fa:
+      type: file
+      description: FA map.
+      pattern: "*.{nii,nii.gz}"
+
+  - md:
+      type: file
+      description: MD map.
+      pattern: "*.{nii,nii.gz}"
+
+  - frf:
+      type: file
+      description: Fiber Response Function (FRF).
+      pattern: "*.txt"
+
+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"
+
+  - fodf:
+      type: file
+      description: FODF map.
+      pattern: "*fodf.nii.gz"
+
+  - peaks:
+      type: file
+      description: Peaks file.
+      pattern: "*peaks.nii.gz"
+
+  - peak_indices:
+      type: file
+      description: Peak indices file.
+      pattern: "*peak_indices.nii.gz"
+
+  - afd_max:
+      type: file
+      description: Maximum Apparent Fiber Density (AFDmax) map.
+      pattern: "*afd_max.nii.gz"
+
+  - afd_total:
+      type: file
+      description: Total Apparent Fiber Density (AFDtotal) map.
+      pattern: "*afd_total.nii.gz"
+
+  - afd_sum:
+      type: file
+      description: Sum of all Apparent Fiber Density (Afdsum) map.
+      pattern: "*afd_sum.nii.gz"
+
+  - nufo:
+      type: file
+      description: Number of Fiber Orientation (NuFO) map.
+      pattern: "*nufo.nii.gz"
+
+authors:
+  - "@gagnonanthony"
diff --git a/modules/nf-scil/reconst/frf/main.nf b/modules/nf-scil/reconst/frf/main.nf
new file mode 100644
index 0000000..7e38569
--- /dev/null
+++ b/modules/nf-scil/reconst/frf/main.nf
@@ -0,0 +1,64 @@
+
+
+process RECONST_FRF {
+    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), path(mask)
+
+    output:
+        tuple val(meta), path("*__frf.txt")             , emit: frf
+        path "versions.yml"                             , emit: versions
+
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def fa = task.ext.fa ? "--fa " + task.ext.fa : ""
+    def fa_min = task.ext.fa_min ? "--min_fa " + task.ext.fa_min : ""
+    def nvox_min = task.ext.nvox_min ? "--min_nvox " + task.ext.nvox_min : ""
+    def roi_radius = task.ext.roi_radius ? "--roi_radii " + task.ext.roi_radius : ""
+    def fix_frf = task.ext.manual_frf ? task.ext.manual_frf : ""
+    def set_mask = mask ? "--mask $mask" : ""
+
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+    export OMP_NUM_THREADS=1
+    export OPENBLAS_NUM_THREADS=1
+
+    scil_compute_ssst_frf.py $dwi $bval $bvec ${prefix}__frf.txt \
+        $set_mask $fa $fa_min $nvox_min $roi_radius --force_b0_threshold
+
+    if ( "$task.ext.set_frf" = true ); then
+        scil_set_response_function.py ${prefix}__frf.txt "${fix_frf}" \
+            ${prefix}__frf.txt -f
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: 1.6.0
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    
+    """
+    scil_compute_ssst_frf.py -h
+    scil_set_response_function.py -h
+
+    touch ${prefix}__frf.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: 1.6.0
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-scil/reconst/frf/meta.yml b/modules/nf-scil/reconst/frf/meta.yml
new file mode 100644
index 0000000..384e835
--- /dev/null
+++ b/modules/nf-scil/reconst/frf/meta.yml
@@ -0,0 +1,63 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "reconst_frf"
+description: Compute a single Fiber Response Function from a DWI.
+keywords:
+  - DWI
+  - FRF
+
+tools:
+  - "DIPY":
+      description: "DIPY is the paragon 3D/4D+ imaging library in Python."
+      homepage: https://dipy.org
+
+  - "Scilpy":
+      description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
+      homepage: "https://github.com/scilus/scilpy.git"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+  
+  - dwi:
+      type: file
+      description: Nifti image of DWI.
+      pattern: "*.{nii,nii.gz}"
+
+  - bval:
+      type: file
+      description: B-values in FSL format.
+      pattern: "*.bval"
+
+  - bvec:
+      type: file
+      description: B-vectors in FSL format.
+      pattern: "*.bvec"
+
+  - mask:
+      type: file
+      description: Nifti b0 binary mask.
+      pattern: "*.{nii,nii.gz}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+  
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  
+  - frf:
+      type: file
+      description: Fiber Response Function (FRF).
+      pattern: "*.txt"
+      
+authors:
+  - "@Manonedde"
diff --git a/modules/nf-scil/tracking/pfttracking/main.nf b/modules/nf-scil/tracking/pfttracking/main.nf
new file mode 100644
index 0000000..3e9eb59
--- /dev/null
+++ b/modules/nf-scil/tracking/pfttracking/main.nf
@@ -0,0 +1,131 @@
+
+process TRACKING_PFTTRACKING {
+    tag "$meta.id"
+    label 'process_single'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
+        'scilus/scilus:1.6.0' }"
+
+    input:
+        tuple val(meta), path(wm), path(gm), path(csf), path(fodf), path(fa)
+
+    output:
+
+        tuple val(meta), path("*__pft_tracking.trk")            , emit: trk
+        tuple val(meta), path("*__pft_tracking_config.json")    , emit: config
+        tuple val(meta), path("*__map_include.nii.gz")          , emit: include
+        tuple val(meta), path("*__map_exclude.nii.gz")          , emit: exclude
+        tuple val(meta), path("*__pft_seeding_mask.nii.gz")     , emit: seeding
+        path "versions.yml"                                     , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def pft_fa_threshold = task.ext.pft_fa_seeding_mask_threshold ? task.ext.pft_fa_seeding_mask_threshold : ""
+    def pft_seeding_mask = task.ext.pft_seeding_mask_type ? "${task.ext.pft_seeding_mask_type}" : ""
+
+    def pft_random_seed = task.ext.pft_random_seed ? "--seed " + task.ext.pft_random_seed : ""
+    def compress = task.ext.pft_compress_streamlines ? "--compress " + task.ext.pft_compress_value : ""
+    def pft_algo = task.ext.pft_algo ? "--algo " + task.ext.pft_algo: ""
+    def pft_seeding_type = task.ext.pft_seeding ? "--"  + task.ext.pft_seeding : ""
+    def pft_nbr_seeds = task.ext.pft_nbr_seeds ? ""  + task.ext.pft_nbr_seeds : ""
+    def pft_step = task.ext.pft_step ? "--step "  + task.ext.pft_step : ""
+    def pft_theta = task.ext.pft_theta ? "--theta "  + task.ext.pft_theta : ""
+    def pft_sfthres = task.ext.pft_sfthres ? "--sfthres "  + task.ext.pft_sfthres : ""
+    def pft_sfthres_init = task.ext.pft_sfthres_init ? "--sfthres_init "  + task.ext.pft_sfthres_init : ""
+    def pft_min_len = task.ext.pft_min_len ? "--min_length "  + task.ext.pft_min_len : ""
+    def pft_max_len = task.ext.pft_max_len ? "--max_length "  + task.ext.pft_max_len : ""
+    def pft_particles = task.ext.pft_particles ? "--particles "  + task.ext.pft_particles : ""
+    def pft_back = task.ext.pft_back ? "--back "  + task.ext.pft_back : ""
+    def pft_front = task.ext.pft_front ? "--forward "  + task.ext.pft_front : ""
+    def basis = task.ext.basis ? "--sh_basis "  + task.ext.basis : ""
+
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+    export OMP_NUM_THREADS=1
+    export OPENBLAS_NUM_THREADS=1
+
+    scil_compute_maps_for_particle_filter_tracking.py $wm $gm $csf \
+        --include ${prefix}__map_include.nii.gz \
+        --exclude ${prefix}__map_exclude.nii.gz \
+        --interface ${prefix}__interface.nii.gz -f
+
+    if [ "${pft_seeding_mask}" == "wm" ]; then
+        scil_image_math.py convert $wm ${prefix}__mask_wm.nii.gz \
+            --data_type uint8
+        scil_image_math.py union ${prefix}__mask_wm.nii.gz \
+            ${prefix}__interface.nii.gz ${prefix}__pft_seeding_mask.nii.gz\
+            --data_type uint8
+
+    elif [ "${pft_seeding_mask}" == "interface" ]; then
+        cp ${prefix}__interface.nii.gz ${prefix}__pft_seeding_mask.nii.gz
+
+    elif [ "${pft_seeding_mask}" == "fa" ]; then
+        mrcalc $fa $pft_fa_threshold -ge ${prefix}__pft_seeding_mask.nii.gz\
+          -datatype uint8
+    fi
+
+    scil_compute_pft.py $fodf ${prefix}__pft_seeding_mask.nii.gz \
+        ${prefix}__map_include.nii.gz ${prefix}__map_exclude.nii.gz tmp.trk\
+        $pft_algo $pft_seeding_type $pft_nbr_seeds \
+        $pft_random_seed $pft_step $pft_theta\
+        $pft_sfthres $pft_sfthres_init $pft_min_len $pft_max_len\
+        $pft_particles $pft_back $pft_front $compress $basis
+
+    scil_remove_invalid_streamlines.py tmp.trk ${prefix}__pft_tracking.trk\
+        --remove_single_point
+
+    cat <<-TRACKING_INFO > ${prefix}__pft_tracking_config.json
+    {"algorithm": "${task.ext.pft_algo}",
+    "seeding_type": "${task.ext.pft_seeding}",
+    "nb_seed": $task.ext.pft_nbr_seeds,
+    "seeding_mask": "${pft_seeding_mask}",
+    "random_seed": $task.ext.pft_random_seed,
+    "is_compress": "${task.ext.pft_compress_streamlines}",
+    "compress_value": $task.ext.pft_compress_value,
+    "step": $task.ext.pft_step,
+    "theta": $task.ext.pft_theta,
+    "sfthres": $task.ext.pft_sfthres,
+    "sfthres_init": $task.ext.pft_sfthres_init,
+    "min_len": $task.ext.pft_min_len,
+    "max_len": $task.ext.pft_max_len,
+    "particles": $task.ext.pft_particles,
+    "back": $task.ext.pft_back,
+    "forward": $task.ext.pft_front,
+    "sh_basis": "${task.ext.basis}"}
+    TRACKING_INFO
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: 1.6.0
+        mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    
+    """
+    scil_compute_pft.py -h
+    scil_compute_maps_for_particle_filter_tracking.py -h
+    scil_image_math.py -h
+    mrcalc -h
+    scil_remove_invalid_streamlines.py -h
+
+    touch ${prefix}__map_include.nii.gz
+    touch ${prefix}__map_exclude.nii.gz
+    touch ${prefix}__pft_seeding_mask.nii.gz
+    touch ${prefix}__pft_tracking.trk
+    touch ${prefix}__pft_tracking_config.json
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: 1.6.0
+        mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-scil/tracking/pfttracking/meta.yml b/modules/nf-scil/tracking/pfttracking/meta.yml
new file mode 100644
index 0000000..a7f6e3a
--- /dev/null
+++ b/modules/nf-scil/tracking/pfttracking/meta.yml
@@ -0,0 +1,91 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "tracking_pfttracking"
+description: Compute include and exclude maps, and the seeding mask
+             from partial volume estimation (PVE) maps.
+             Generates a tractogram using anatomically-constrained particle
+             filter tracking, Particle Filtering Tractography (PFT).
+keywords:
+  - PFT
+  - tractography
+
+tools:
+  - "DIPY":
+      description: "DIPY is the paragon 3D/4D+ imaging library in Python."
+      homepage: https://dipy.org
+      doi: "10.1016/j.neuroimage.2014.04.074"
+  - "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 ]`
+
+  - wm:
+      type: file
+      description: Nifti white matter probability map.
+      pattern: "*.{nii,nii.gz}"
+
+  - gm:
+      type: file
+      description: Nifti grey matter probability map.
+      pattern: "*.{nii,nii.gz}"
+
+  - csf:
+      type: file
+      description: Nifti cerebrospinal fuild probability map.
+      pattern: "*.{nii,nii.gz}"
+
+  - fodf:
+      type: file
+      description: Nifti image of Spherical harmonic file (fodf).
+      pattern: "*.{nii,nii.gz}"
+
+  - fa:
+      type: file
+      description: Nifti image of FA.
+      pattern: "*.{nii,nii.gz}"
+
+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"
+
+  - include:
+      type: file
+      description: Nifti probability map for tracking of ending the streamline and including it in the output.
+      pattern: "*.{nii,nii.gz}"
+
+  - exclude:
+      type: file
+      description: Nifti probability map for tracking of ending the streamline and excluding it in the output.
+      pattern: "*.{nii,nii.gz}"
+
+  - seeding:
+      type: file
+      description: Nifti seeding mask for tracking.
+      pattern: "*.{nii,nii.gz}"
+
+  - trk:
+      type: file
+      description: Tractogram output file.
+      pattern: "*.{trk,tck}"
+
+  - config:
+      type: file
+      description: Json file containing tracking parameters.
+      pattern: "*.{json}"
+
+authors:
+  - "@Manonedde"
diff --git a/modules/nf-scil/utils/extractb0/main.nf b/modules/nf-scil/utils/extractb0/main.nf
new file mode 100644
index 0000000..d79b57a
--- /dev/null
+++ b/modules/nf-scil/utils/extractb0/main.nf
@@ -0,0 +1,54 @@
+
+
+process UTILS_EXTRACTB0 {
+    tag "$meta.id"
+    label 'process_single'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://scil.usherbrooke.ca/containers/scilus_1.6.0.sif':
+        'scilus/scilus:1.6.0' }"
+
+    input:
+    tuple val(meta), path(dwi), path(bval), path(bvec)
+
+    output:
+    tuple val(meta), path("*_b0*.nii.gz"), emit: b0
+    path "versions.yml"                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def extraction_strategy = task.ext.b0_extraction_strategy ? "--$task.ext.b0_extraction_strategy" : "--mean"
+    def b0_threshold = task.ext.b0_threshold ? "--b0_thr $task.ext.b0_threshold" : ""
+    def output_series = task.ext.output_series ? "" : "--single-image"
+    """
+    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 \
+        $output_series $extraction_strategy $b0_threshold --force_b0_threshold
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: 1.6.0
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    
+    """
+    scil_extract_b0.py - h
+
+    touch ${prefix}_b0.nii.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: 1.6.0
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-scil/utils/extractb0/meta.yml b/modules/nf-scil/utils/extractb0/meta.yml
new file mode 100644
index 0000000..8834184
--- /dev/null
+++ b/modules/nf-scil/utils/extractb0/meta.yml
@@ -0,0 +1,56 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "utils_extractb0"
+description: Extract a b0 volume from a DWI image.
+keywords:
+  - dwi
+  - extract
+  - b0
+tools:
+  - "Scilpy":
+      description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
+      homepage: "https://github.com/scilus/scilpy.git"
+
+input:
+  # Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+  
+  - dwi:
+      type: file
+      description: Nifti DWI volume to perform BET + crop.
+      pattern: "*.{nii,nii.gz}"
+
+  - bval:
+      type: file
+      description: B-values in FSL format.
+      pattern: "*.bval"
+
+  - bvec:
+      type: file
+      description: B-vectors in FSL format.
+      pattern: "*.bvec"
+
+output:
+  #Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+  
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  
+  - b0:
+      type: file
+      description: b0 image(s) extracted from the DWI
+      pattern: "*_b0*.{nii,nii.gz}"
+
+authors:
+  - "@AlexVCaron"
diff --git a/nextflow.config b/nextflow.config
index b52ed35..ec399fb 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -1,270 +1,82 @@
-/*
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    nf-core/fibercup Nextflow config file
-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-    Default config options for all compute environments
-----------------------------------------------------------------------------------------
-*/
+process {
+    publishDir = {"./Results_Fiber_Cup/${task.process}"}
+    scratch = true
+    errorStrategy = { task.attempt <= 3 ? 'retry' : 'ignore' }
+    maxRetries = 3
+    maxErrors = -1
+    stageInMode = 'copy'
+    stageOutMode = 'rsync'
+    tag = { "$sid" }
+    afterScript = 'sleep 1'
+}
 
-// Global default params, used in configs
 params {
 
-    // TODO nf-core: Specify your pipeline's command line flags
-    // Input options
-    input                      = null
-    // References
-    genome                     = null
-    igenomes_base              = 's3://ngi-igenomes/igenomes'
-    igenomes_ignore            = false
-    
-
-    // MultiQC options
-    multiqc_config             = null
-    multiqc_title              = null
-    multiqc_logo               = null
-    max_multiqc_email_size     = '25.MB'
-    multiqc_methods_description = null
-
-    // Boilerplate options
-    outdir                     = null
-    publish_dir_mode           = 'copy'
-    email                      = null
-    email_on_fail              = null
-    plaintext_email            = false
-    monochrome_logs            = false
-    hook_url                   = null
-    help                       = false
-    version                    = false
-
-    // Config options
-    config_profile_name        = null
-    config_profile_description = null
-    custom_config_version      = 'master'
-    custom_config_base         = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}"
-    config_profile_contact     = null
-    config_profile_url         = null
-    
-
-    // Max resource options
-    // Defaults only, expecting to be overwritten
-    max_memory                 = '128.GB'
-    max_cpus                   = 16
-    max_time                   = '240.h'
-
-    // Schema validation default options
-    validationFailUnrecognisedParams = false
-    validationLenientMode            = false
-    validationSchemaIgnoreParams     = 'genomes,igenomes_base'
-    validationShowHiddenParams       = false
-    validate_params                  = true
+    //** DENOISING DWI Options **//
+    extent = 3
+
+    //** DTI Options **//
+    ad = false
+    evecs = false
+    evals = false
+    fa = true
+    ga = false
+    rgb = false
+    md = true
+    mode = false
+    norm = false
+    rd = false
+    tensor = false
+    nonphysical = false
+    pulsation = false
+    residual = false
+
+    //** FRF Options **//
+    fa=0.7
+    min_fa=0.5
+    min_nvox=300
+    roi_radius=20
+    set_frf=true
+    manual_frf="15,4,4"
+
+    //** FODF Options **//
+    b0_thr_extract_b0 = 10
+    dwi_shell_tolerance = 20
+    min_fodf_shell_value = 700
+    sh_order = 8
+    sh_basis = "descoteaux07"
+    fa_threshold = 0.1
+    md_threshold = 0.003
+    relative_threshold = 0.1
+    processes = 4
+    peaks = false
+    peak_indices = false
+    afd_max = false
+    afd_total = false
+    afd_sum = false
+    nufo = false
+
+    //** LOCALTRACKING Options **//
+    local_compress_streamlines=true
+    local_algo="prob"
+    local_seeding="npv"
+    local_nbr_seeds=10
+    local_step=0.5
+    local_theta=20
+    local_sfthres=0.1
+    local_sfthres_init=0.5
+    local_min_len=20
+    local_max_len=200
+    local_compress_value=0.2
+    local_random_seed=0
 
 }
 
-// Load base.config by default for all pipelines
-includeConfig 'conf/base.config'
-
-// Load nf-core custom profiles from different Institutions
-try {
-    includeConfig "${params.custom_config_base}/nfcore_custom.config"
-} catch (Exception e) {
-    System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config")
-}
 
-// Load nf-core/fibercup custom profiles from different institutions.
-// Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs!
-// try {
-//   includeConfig "${params.custom_config_base}/pipeline/fibercup.config"
-// } catch (Exception e) {
-//   System.err.println("WARNING: Could not load nf-core/config/fibercup profiles: ${params.custom_config_base}/pipeline/fibercup.config")
-// }
 profiles {
-    debug {
-        dumpHashes             = true
-        process.beforeScript   = 'echo $HOSTNAME'
-        cleanup                = false
-    }
-    conda {
-        conda.enabled          = true
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
-    }
-    mamba {
-        conda.enabled          = true
-        conda.useMamba         = true
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
-    }
-    docker {
-        docker.enabled         = true
-        docker.userEmulation   = true
-        conda.enabled          = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
-    }
-    arm {
-        docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
-    }
-    singularity {
-        singularity.enabled    = true
-        singularity.autoMounts = true
-        conda.enabled          = false
-        docker.enabled         = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
-    }
-    podman {
-        podman.enabled         = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
-    }
-    shifter {
-        shifter.enabled        = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
-    }
-    charliecloud {
-        charliecloud.enabled   = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        apptainer.enabled      = false
-    }
-    apptainer {
-        apptainer.enabled      = true
-        apptainer.autoMounts   = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-    }
-    gitpod {
-        executor.name          = 'local'
-        executor.cpus          = 4
-        executor.memory        = 8.GB
-    }
-    test      { includeConfig 'conf/test.config'      }
-    test_full { includeConfig 'conf/test_full.config' }
-}
-
-// Set default registry for Apptainer, Docker, Podman and Singularity independent of -profile
-// Will not be used unless Apptainer / Docker / Podman / Singularity are enabled
-// Set to your registry if you have a mirror of containers
-apptainer.registry   = 'quay.io'
-docker.registry      = 'quay.io'
-podman.registry      = 'quay.io'
-singularity.registry = 'quay.io'
-
-// Nextflow plugins
-plugins {
-    id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet
-}
-
-// Load igenomes.config if required
-if (!params.igenomes_ignore) {
-    includeConfig 'conf/igenomes.config'
-} else {
-    params.genomes = [:]
-}
-// Export these variables to prevent local Python/R libraries from conflicting with those in the container
-// The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container.
-// See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable.
-
-env {
-    PYTHONNOUSERSITE = 1
-    R_PROFILE_USER   = "/.Rprofile"
-    R_ENVIRON_USER   = "/.Renviron"
-    JULIA_DEPOT_PATH = "/usr/local/share/julia"
-}
-
-// Capture exit codes from upstream processes when piping
-process.shell = ['/bin/bash', '-euo', 'pipefail']
-
-def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss')
-timeline {
-    enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_timeline_${trace_timestamp}.html"
-}
-report {
-    enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_report_${trace_timestamp}.html"
-}
-trace {
-    enabled = true
-    file    = "${params.outdir}/pipeline_info/execution_trace_${trace_timestamp}.txt"
-}
-dag {
-    enabled = true
-    file    = "${params.outdir}/pipeline_info/pipeline_dag_${trace_timestamp}.html"
-}
-
-manifest {
-    name            = 'nf-core/fibercup'
-    author          = """stan"""
-    homePage        = 'https://github.com/nf-core/fibercup'
-    description     = """test for the new nf-scil pipeline"""
-    mainScript      = 'main.nf'
-    nextflowVersion = '!>=23.04.0'
-    version         = '1.0dev'
-    doi             = ''
-}
-
-// Load modules.config for DSL2 module specific options
-includeConfig 'conf/modules.config'
-
-// Function to ensure that resource requirements don't go beyond
-// a maximum limit
-def check_max(obj, type) {
-    if (type == 'memory') {
-        try {
-            if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
-                return params.max_memory as nextflow.util.MemoryUnit
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'time') {
-        try {
-            if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
-                return params.max_time as nextflow.util.Duration
-            else
-                return obj
-        } catch (all) {
-            println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
-            return obj
-        }
-    } else if (type == 'cpus') {
-        try {
-            return Math.min( obj, params.max_cpus as int )
-        } catch (all) {
-            println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
-            return obj
+    no_symlink {
+        process{
+            publishDir = [path: {"./Results_Fiber_Cup/${task.process}"}, mode: 'copy']
         }
     }
-}
+}
\ No newline at end of file