From d26bf894e57df8bef66530f6ce566dae9b7255e5 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Thu, 8 Feb 2024 09:23:53 -0500
Subject: [PATCH 01/18] Initial creation

---
 .../nf-scil/segmentation/fsreconall/main.nf   | 91 +++++++++++++++++++
 .../nf-scil/segmentation/fsreconall/meta.yml  | 55 +++++++++++
 tests/config/pytest_modules.yml               |  4 +
 .../nf-scil/segmentation/fsreconall/main.nf   | 15 +++
 .../segmentation/fsreconall/nextflow.config   |  5 +
 .../nf-scil/segmentation/fsreconall/test.yml  | 13 +++
 6 files changed, 183 insertions(+)
 create mode 100644 modules/nf-scil/segmentation/fsreconall/main.nf
 create mode 100644 modules/nf-scil/segmentation/fsreconall/meta.yml
 create mode 100644 tests/modules/nf-scil/segmentation/fsreconall/main.nf
 create mode 100644 tests/modules/nf-scil/segmentation/fsreconall/nextflow.config
 create mode 100644 tests/modules/nf-scil/segmentation/fsreconall/test.yml

diff --git a/modules/nf-scil/segmentation/fsreconall/main.nf b/modules/nf-scil/segmentation/fsreconall/main.nf
new file mode 100644
index 00000000..e072a0c4
--- /dev/null
+++ b/modules/nf-scil/segmentation/fsreconall/main.nf
@@ -0,0 +1,91 @@
+// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
+//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
+//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
+//               https://nf-co.re/join
+// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
+//               All other parameters MUST be provided using the "task.ext" directive, see here:
+//               https://www.nextflow.io/docs/latest/process.html#ext
+//               where "task.ext" is a string.
+//               Any parameters that need to be evaluated in the context of a particular sample
+//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
+// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
+//               unless there is a run-time, storage advantage in implementing in this way
+//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
+//                 bwa mem | samtools view -B -T ref.fasta
+// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
+//               list (`[]`) instead of a file can be used to work around this issue.
+
+process SEGMENTATION_FSRECONALL {
+    tag "$meta.id"
+    label 'process_single'
+
+    // TODO nf-core: List required Conda package(s).
+    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
+    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
+    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
+    conda "YOUR-TOOL-HERE"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
+        'biocontainers/YOUR-TOOL-HERE' }"
+
+    input:
+    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
+    //               MUST be provided as an input via a Groovy Map called "meta".
+    //               This information may not be required in some instances e.g. indexing reference genome files:
+    //               https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf
+    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
+    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
+    tuple val(meta), path(bam)
+
+    output:
+    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
+    tuple val(meta), path("*.bam"), emit: bam
+    // TODO nf-core: List additional required output channels/values here
+    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}"
+    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
+    //               If the software is unable to output a version number on the command-line then it can be manually specified
+    //               e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf
+    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
+    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
+    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
+    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
+    // TODO nf-core: Please replace the example samtools command below with your module's command
+    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
+    """
+    samtools \\
+        sort \\
+        $args \\
+        -@ $task.cpus \\
+        -o ${prefix}.bam \\
+        -T $prefix \\
+        $bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        : \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
+    //               Have a look at the following examples:
+    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
+    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
+    """
+    touch ${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        : \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-scil/segmentation/fsreconall/meta.yml b/modules/nf-scil/segmentation/fsreconall/meta.yml
new file mode 100644
index 00000000..db0e37b4
--- /dev/null
+++ b/modules/nf-scil/segmentation/fsreconall/meta.yml
@@ -0,0 +1,55 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
+name: "segmentation_fsreconall"
+## TODO nf-core: Add a description of the module and list keywords
+description: write your description here
+keywords:
+  - sort
+  - example
+  - genomics
+tools:
+  - "segmentation":
+      ## TODO nf-core: Add a description and other details for the software below
+      description: ""
+      homepage: ""
+      documentation: ""
+      tool_dev_url: ""
+      doi: ""
+      licence: ""
+
+## TODO nf-core: Add a description of all of the variables used as input
+input:
+  # Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+  
+  ## TODO nf-core: Delete / customise this example input
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+## TODO nf-core: Add a description of all of the variables used as output
+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"
+  ## TODO nf-core: Delete / customise this example output
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+authors:
+  - "@EmmaRenauld"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 0bc4b7f1..855e3825 100755
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -13,3 +13,7 @@ testdata/scilpy:
 testdata/sizeof:
   - modules/nf-scil/testdata/sizeof/**
   - tests/modules/nf-scil/testdata/sizeof/**
+
+segmentation/fsreconall:
+  - modules/nf-scil/segmentation/fsreconall/**
+  - tests/modules/nf-scil/segmentation/fsreconall/**
diff --git a/tests/modules/nf-scil/segmentation/fsreconall/main.nf b/tests/modules/nf-scil/segmentation/fsreconall/main.nf
new file mode 100644
index 00000000..abb985ea
--- /dev/null
+++ b/tests/modules/nf-scil/segmentation/fsreconall/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { SEGMENTATION_FSRECONALL } from '../../../../../modules/nf-scil/segmentation/fsreconall/main.nf'
+
+workflow test_segmentation_fsreconall {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    SEGMENTATION_FSRECONALL ( input )
+}
diff --git a/tests/modules/nf-scil/segmentation/fsreconall/nextflow.config b/tests/modules/nf-scil/segmentation/fsreconall/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/nf-scil/segmentation/fsreconall/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}
\ No newline at end of file
diff --git a/tests/modules/nf-scil/segmentation/fsreconall/test.yml b/tests/modules/nf-scil/segmentation/fsreconall/test.yml
new file mode 100644
index 00000000..0c0efed4
--- /dev/null
+++ b/tests/modules/nf-scil/segmentation/fsreconall/test.yml
@@ -0,0 +1,13 @@
+## TODO nf-core: Please run the following command to build this file:
+#                nf-core modules create-test-yml /fsreconall
+- name: "segmentation fsreconall"
+  command: nextflow run ./tests/modules/nf-scil/segmentation/fsreconall -entry test_segmentation_fsreconall -c ./tests/config/nextflow.config
+  tags:
+    - "segmentation"
+    - "segmentation/fsreconall"
+  files:
+    - path: "output/segmentation/test.bam"
+      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: "output/segmentation/versions.yml"
+      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b
+    

From 9e75cdd0afec9229e459a26149636bff83c4dc14 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Thu, 8 Feb 2024 09:50:29 -0500
Subject: [PATCH 02/18] Edit main.nf

---
 .../nf-scil/segmentation/fsreconall/main.nf   | 74 ++++---------------
 1 file changed, 14 insertions(+), 60 deletions(-)

diff --git a/modules/nf-scil/segmentation/fsreconall/main.nf b/modules/nf-scil/segmentation/fsreconall/main.nf
index e072a0c4..d9b9d681 100644
--- a/modules/nf-scil/segmentation/fsreconall/main.nf
+++ b/modules/nf-scil/segmentation/fsreconall/main.nf
@@ -1,91 +1,45 @@
-// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
-//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
-//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
-//               https://nf-co.re/join
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-//               All other parameters MUST be provided using the "task.ext" directive, see here:
-//               https://www.nextflow.io/docs/latest/process.html#ext
-//               where "task.ext" is a string.
-//               Any parameters that need to be evaluated in the context of a particular sample
-//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
-//               unless there is a run-time, storage advantage in implementing in this way
-//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
-//                 bwa mem | samtools view -B -T ref.fasta
-// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
-//               list (`[]`) instead of a file can be used to work around this issue.
-
 process SEGMENTATION_FSRECONALL {
     tag "$meta.id"
     label 'process_single'
 
-    // TODO nf-core: List required Conda package(s).
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
-    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
-    conda "YOUR-TOOL-HERE"
+    # TODO Voir comment ajouter FreeSurfer!
+    # Note. Freesurfer is already on Docker. See documentation on
+    # https://hub.docker.com/r/freesurfer/freesurfer
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
-        'biocontainers/YOUR-TOOL-HERE' }"
+        freesurfer/freesurfer:7.1.1}"
 
     input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
-    //               MUST be provided as an input via a Groovy Map called "meta".
-    //               This information may not be required in some instances e.g. indexing reference genome files:
-    //               https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf
-    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
-    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
-    tuple val(meta), path(bam)
+        tuple val(meta), path(anat)
 
     output:
-    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
-    tuple val(meta), path("*.bam"), emit: bam
-    // TODO nf-core: List additional required output channels/values here
-    path "versions.yml"           , emit: versions
+        path("*__recon_all")                    , emit: recon_all_out_folder
+        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}"
-    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
-    //               If the software is unable to output a version number on the command-line then it can be manually specified
-    //               e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf
-    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    // TODO nf-core: Please replace the example samtools command below with your module's command
-    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
     """
-    samtools \\
-        sort \\
-        $args \\
-        -@ $task.cpus \\
-        -o ${prefix}.bam \\
-        -T $prefix \\
-        $bam
+    export SUBJECTS_DIR=.
+    recon-all -i $anat -s ${prefix}__recon_all -all -parallel -openmp $params.nb_threads
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        : \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
+        freesurfer: 7.1.1
     END_VERSIONS
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
-    //               Have a look at the following examples:
-    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
-    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
     """
-    touch ${prefix}.bam
+    recon-all -help
+
+    mkdir ${prefix}__recon_all
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        : \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
+        freesurfer: 7.1.1
     END_VERSIONS
     """
 }

From d19f4a33e93d5538b4501b053b1a5d0167c7d227 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Thu, 8 Feb 2024 10:00:03 -0500
Subject: [PATCH 03/18] Prepare the test

---
 tests/config/test_data.config                         | 3 +++
 tests/modules/nf-scil/segmentation/fsreconall/main.nf | 7 +++++--
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index f34a7443..88e1037a 100755
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -88,6 +88,9 @@ params {
             "fastseg" {
                 image = "${params.test_data_base}/heavy/anat/anat_image.nii.gz"
             }
+            "fsreconall" {
+                anat = "${params.test_data_base}/heavy/anat/anat_image.nii.gz"
+            }
         }
         "tracking" {
             "pfttracking" {
diff --git a/tests/modules/nf-scil/segmentation/fsreconall/main.nf b/tests/modules/nf-scil/segmentation/fsreconall/main.nf
index abb985ea..28a4ccc3 100644
--- a/tests/modules/nf-scil/segmentation/fsreconall/main.nf
+++ b/tests/modules/nf-scil/segmentation/fsreconall/main.nf
@@ -5,11 +5,14 @@ nextflow.enable.dsl = 2
 include { SEGMENTATION_FSRECONALL } from '../../../../../modules/nf-scil/segmentation/fsreconall/main.nf'
 
 workflow test_segmentation_fsreconall {
-    
+
+    # Too long, we don't test.
+    # To test locally, uncomment the following lines:
     input = [
         [ id:'test', single_end:false ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+        file(params.test_data['segmentation']['fsreconall']['anat'], checkIfExists: true)
     ]
 
     SEGMENTATION_FSRECONALL ( input )
+
 }

From 8266da291f0f5c610181222872c6defb32a160b7 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Thu, 8 Feb 2024 10:27:13 -0500
Subject: [PATCH 04/18] Edit meta.yml file

---
 .../nf-scil/segmentation/fsreconall/meta.yml  | 46 +++++++------------
 1 file changed, 17 insertions(+), 29 deletions(-)

diff --git a/modules/nf-scil/segmentation/fsreconall/meta.yml b/modules/nf-scil/segmentation/fsreconall/meta.yml
index db0e37b4..afa91888 100644
--- a/modules/nf-scil/segmentation/fsreconall/meta.yml
+++ b/modules/nf-scil/segmentation/fsreconall/meta.yml
@@ -1,55 +1,43 @@
 ---
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: "segmentation_fsreconall"
-## TODO nf-core: Add a description of the module and list keywords
-description: write your description here
+description: "Performs Freesurfer's recon-all script to segment your anatomy (probably a T1) into labels, surfaces, and much more. See the full documentation here: https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all."
 keywords:
-  - sort
-  - example
-  - genomics
+  - FreeSurfer
+  - Segmentation
+  - Tissues
 tools:
-  - "segmentation":
-      ## TODO nf-core: Add a description and other details for the software below
-      description: ""
-      homepage: ""
-      documentation: ""
-      tool_dev_url: ""
-      doi: ""
-      licence: ""
+  - "Freesurfer":
+      description: "An open source neuroimaging toolkit for processing, analyzing, and visualizing human brain MR images."
+      homepage: "https://surfer.nmr.mgh.harvard.edu/"
 
-## TODO nf-core: Add a description of all of the variables used as input
 input:
-  # Only when we have meta
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. `[ id:'test', single_end:false ]`
-  
-  ## TODO nf-core: Delete / customise this example input
-  - bam:
+
+  - anat:
       type: file
-      description: Sorted BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
+      description: An anatomy (ex, .nii.gz).
+      pattern: "*.mgz"
 
-## TODO nf-core: Add a description of all of the variables used as output
 output:
-  #Only when we have meta
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. `[ id:'test', single_end:false ]`
-  
+
+  - recon_all_out_folder:
+      type: directory
+      description: Directory containing all recon-all outputs.
+      pattern: "*.{nii,nii.gz}"
+
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  ## TODO nf-core: Delete / customise this example output
-  - bam:
-      type: file
-      description: Sorted BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
 
 authors:
   - "@EmmaRenauld"

From fc42da170194d55b03e581a50c437d9450b4bc8e Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Thu, 8 Feb 2024 11:13:30 -0500
Subject: [PATCH 05/18] Fix test.

---
 modules/nf-scil/segmentation/fsreconall/main.nf     | 13 +++++++------
 .../modules/nf-scil/segmentation/fsreconall/main.nf |  6 ++++--
 .../nf-scil/segmentation/fsreconall/nextflow.config |  3 +--
 3 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/modules/nf-scil/segmentation/fsreconall/main.nf b/modules/nf-scil/segmentation/fsreconall/main.nf
index d9b9d681..1c882ac6 100644
--- a/modules/nf-scil/segmentation/fsreconall/main.nf
+++ b/modules/nf-scil/segmentation/fsreconall/main.nf
@@ -2,11 +2,9 @@ process SEGMENTATION_FSRECONALL {
     tag "$meta.id"
     label 'process_single'
 
-    # TODO Voir comment ajouter FreeSurfer!
-    # Note. Freesurfer is already on Docker. See documentation on
-    # https://hub.docker.com/r/freesurfer/freesurfer
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        freesurfer/freesurfer:7.1.1}"
+    // Note. Freesurfer is already on Docker. See documentation on
+    // https://hub.docker.com/r/freesurfer/freesurfer
+    container "freesurfer/freesurfer:7.1.1"
 
     input:
         tuple val(meta), path(anat)
@@ -18,11 +16,14 @@ process SEGMENTATION_FSRECONALL {
     when:
     task.ext.when == null || task.ext.when
 
+    // Note. In dsl1, we used an additional option:   -parallel -openmp $params.nb_threads.
+    // Removed here.
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     export SUBJECTS_DIR=.
-    recon-all -i $anat -s ${prefix}__recon_all -all -parallel -openmp $params.nb_threads
+
+    recon-all -i $anat -s ${prefix}__recon_all -all
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/tests/modules/nf-scil/segmentation/fsreconall/main.nf b/tests/modules/nf-scil/segmentation/fsreconall/main.nf
index 28a4ccc3..2404e8be 100644
--- a/tests/modules/nf-scil/segmentation/fsreconall/main.nf
+++ b/tests/modules/nf-scil/segmentation/fsreconall/main.nf
@@ -4,10 +4,12 @@ nextflow.enable.dsl = 2
 
 include { SEGMENTATION_FSRECONALL } from '../../../../../modules/nf-scil/segmentation/fsreconall/main.nf'
 
+// Too long, we don't test.
+// To test locally, add the following lines:
+
 workflow test_segmentation_fsreconall {
 
-    # Too long, we don't test.
-    # To test locally, uncomment the following lines:
+
     input = [
         [ id:'test', single_end:false ], // meta map
         file(params.test_data['segmentation']['fsreconall']['anat'], checkIfExists: true)
diff --git a/tests/modules/nf-scil/segmentation/fsreconall/nextflow.config b/tests/modules/nf-scil/segmentation/fsreconall/nextflow.config
index 50f50a7a..83411693 100644
--- a/tests/modules/nf-scil/segmentation/fsreconall/nextflow.config
+++ b/tests/modules/nf-scil/segmentation/fsreconall/nextflow.config
@@ -1,5 +1,4 @@
 process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-    
-}
\ No newline at end of file
+}

From 74e4a57fd7232fa3890223cbcdc6e33a6671fd3d Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Thu, 8 Feb 2024 13:03:16 -0500
Subject: [PATCH 06/18] Add license (optional input)

---
 .test_data/heavy/freesurfer/license.txt       |  3 +++
 .../nf-scil/segmentation/fsreconall/main.nf   | 22 ++++++++++++++++---
 .../nf-scil/segmentation/fsreconall/meta.yml  |  7 +++++-
 tests/config/test_data.config                 |  1 +
 .../nf-scil/segmentation/fsreconall/main.nf   |  3 ++-
 .../nf-scil/segmentation/fsreconall/test.yml  | 14 ++++--------
 6 files changed, 35 insertions(+), 15 deletions(-)
 create mode 100644 .test_data/heavy/freesurfer/license.txt

diff --git a/.test_data/heavy/freesurfer/license.txt b/.test_data/heavy/freesurfer/license.txt
new file mode 100644
index 00000000..9c31cab4
--- /dev/null
+++ b/.test_data/heavy/freesurfer/license.txt
@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:05d2a544719626968d938cca74effbd673474fdc0db1d134f77f38e2fc497f49
+size 102
diff --git a/modules/nf-scil/segmentation/fsreconall/main.nf b/modules/nf-scil/segmentation/fsreconall/main.nf
index 1c882ac6..ae034c0e 100644
--- a/modules/nf-scil/segmentation/fsreconall/main.nf
+++ b/modules/nf-scil/segmentation/fsreconall/main.nf
@@ -7,7 +7,7 @@ process SEGMENTATION_FSRECONALL {
     container "freesurfer/freesurfer:7.1.1"
 
     input:
-        tuple val(meta), path(anat)
+        tuple val(meta), path(anat), path(fs_license) /* optional, value = [] */
 
     output:
         path("*__recon_all")                    , emit: recon_all_out_folder
@@ -21,10 +21,26 @@ process SEGMENTATION_FSRECONALL {
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    export SUBJECTS_DIR=.
-
+    # Manage the license. (Save old one if existed.)
+    if [ $fs_license = [] ]; then
+        echo "License not given in input. Using default environment. "
+    else
+        cp $fs_license .license
+        here=`pwd`
+        export FS_LICENSE=\$here/.license
+    fi
+
+    # Run the main script
+    export SUBJECTS_DIR=`pwd`
     recon-all -i $anat -s ${prefix}__recon_all -all
 
+    # Remove the license
+    if [ ! $fs_license = [] ]; then
+        rm .license
+    fi
+
+
+    # Finish
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         freesurfer: 7.1.1
diff --git a/modules/nf-scil/segmentation/fsreconall/meta.yml b/modules/nf-scil/segmentation/fsreconall/meta.yml
index afa91888..e17b8c0c 100644
--- a/modules/nf-scil/segmentation/fsreconall/meta.yml
+++ b/modules/nf-scil/segmentation/fsreconall/meta.yml
@@ -20,7 +20,12 @@ input:
   - anat:
       type: file
       description: An anatomy (ex, .nii.gz).
-      pattern: "*.mgz"
+      pattern: "*.{nii,nii.gz,mgz}"
+
+  - fs_license:
+      type: file
+      description: The path to your FreeSurfer license. To get one, go to https://surfer.nmr.mgh.harvard.edu/registration.html. Optional. If you have already set your license as prescribed by Freesurfer (copied to a .license file in your $FREESURFER_HOME), this is not required.
+      pattern: "*.txt"
 
 output:
   - meta:
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index 88e1037a..e898e9f1 100755
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -90,6 +90,7 @@ params {
             }
             "fsreconall" {
                 anat = "${params.test_data_base}/heavy/anat/anat_image.nii.gz"
+                license = "${params.test_data_base}/heavy/freesurfer/license.txt"
             }
         }
         "tracking" {
diff --git a/tests/modules/nf-scil/segmentation/fsreconall/main.nf b/tests/modules/nf-scil/segmentation/fsreconall/main.nf
index 2404e8be..95c42d72 100644
--- a/tests/modules/nf-scil/segmentation/fsreconall/main.nf
+++ b/tests/modules/nf-scil/segmentation/fsreconall/main.nf
@@ -12,7 +12,8 @@ workflow test_segmentation_fsreconall {
 
     input = [
         [ id:'test', single_end:false ], // meta map
-        file(params.test_data['segmentation']['fsreconall']['anat'], checkIfExists: true)
+        file(params.test_data['segmentation']['fsreconall']['anat'], checkIfExists: true),
+        file(params.test_data['segmentation']['fsreconall']['license'], checkIfExists: true)
     ]
 
     SEGMENTATION_FSRECONALL ( input )
diff --git a/tests/modules/nf-scil/segmentation/fsreconall/test.yml b/tests/modules/nf-scil/segmentation/fsreconall/test.yml
index 0c0efed4..acd1053d 100644
--- a/tests/modules/nf-scil/segmentation/fsreconall/test.yml
+++ b/tests/modules/nf-scil/segmentation/fsreconall/test.yml
@@ -1,13 +1,7 @@
-## TODO nf-core: Please run the following command to build this file:
-#                nf-core modules create-test-yml /fsreconall
-- name: "segmentation fsreconall"
+- name: segmentation fsreconall test_segmentation_fsreconall
   command: nextflow run ./tests/modules/nf-scil/segmentation/fsreconall -entry test_segmentation_fsreconall -c ./tests/config/nextflow.config
   tags:
-    - "segmentation"
-    - "segmentation/fsreconall"
+    - segmentation/fsreconall
+    - segmentation
   files:
-    - path: "output/segmentation/test.bam"
-      md5sum: e667c7caad0bc4b7ac383fd023c654fc
-    - path: "output/segmentation/versions.yml"
-      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b
-    
+    - path: output/segmentation/versions.yml

From 35a0b94d49943ef631fea80691f0aefb4a5a4f38 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Thu, 8 Feb 2024 14:01:12 -0500
Subject: [PATCH 07/18] WIP

---
 tests/config/test_data.config                      |  2 +-
 .../nf-scil/segmentation/fsreconall/main.nf        | 14 ++++++++++----
 2 files changed, 11 insertions(+), 5 deletions(-)

diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index e898e9f1..0edf1280 100755
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -1,7 +1,7 @@
 
 params {
     // Default endpoint provided by nf-core, we keep it here in case sometimes we end up pushing stuff to them
-    test_data_base = "https://github.com/scilus/nf-scil/raw/main/.test_data"
+    test_data_base = "https://github.com/EmmaRenauld/nf-scil/raw/module_reconall/.test_data"
     test_data {
         "image" {
             "resample" {
diff --git a/tests/modules/nf-scil/segmentation/fsreconall/main.nf b/tests/modules/nf-scil/segmentation/fsreconall/main.nf
index 95c42d72..a0fa1af5 100644
--- a/tests/modules/nf-scil/segmentation/fsreconall/main.nf
+++ b/tests/modules/nf-scil/segmentation/fsreconall/main.nf
@@ -5,17 +5,23 @@ nextflow.enable.dsl = 2
 include { SEGMENTATION_FSRECONALL } from '../../../../../modules/nf-scil/segmentation/fsreconall/main.nf'
 
 // Too long, we don't test.
-// To test locally, add the following lines:
-
-workflow test_segmentation_fsreconall {
+// To test locally, add the following lines to the workflow below:
 
 
+workflow test_segmentation_fsreconall {
     input = [
         [ id:'test', single_end:false ], // meta map
         file(params.test_data['segmentation']['fsreconall']['anat'], checkIfExists: true),
         file(params.test_data['segmentation']['fsreconall']['license'], checkIfExists: true)
     ]
 
-    SEGMENTATION_FSRECONALL ( input )
+    // Hiding the real test because it is too long.
+    // SEGMENTATION_FSRECONALL ( input )
+
+    // But nf-core does not allow an empty test. Results in critical error: Could not find any test result files in '/tmp/xxxxx'.
+    // Creating a fake new file.
+    def file = new File("test__recon_all")
+    file.mkdir()
+
 
 }

From 225c1a2e864e6558616544978580ea3a5be544a0 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Thu, 8 Feb 2024 14:11:32 -0500
Subject: [PATCH 08/18] Removing the test

---
 tests/modules/nf-scil/segmentation/fsreconall/main.nf  | 9 ++-------
 tests/modules/nf-scil/segmentation/fsreconall/test.yml | 2 --
 2 files changed, 2 insertions(+), 9 deletions(-)

diff --git a/tests/modules/nf-scil/segmentation/fsreconall/main.nf b/tests/modules/nf-scil/segmentation/fsreconall/main.nf
index a0fa1af5..56c7f58d 100644
--- a/tests/modules/nf-scil/segmentation/fsreconall/main.nf
+++ b/tests/modules/nf-scil/segmentation/fsreconall/main.nf
@@ -7,7 +7,7 @@ include { SEGMENTATION_FSRECONALL } from '../../../../../modules/nf-scil/segment
 // Too long, we don't test.
 // To test locally, add the following lines to the workflow below:
 
-
+/*
 workflow test_segmentation_fsreconall {
     input = [
         [ id:'test', single_end:false ], // meta map
@@ -18,10 +18,5 @@ workflow test_segmentation_fsreconall {
     // Hiding the real test because it is too long.
     // SEGMENTATION_FSRECONALL ( input )
 
-    // But nf-core does not allow an empty test. Results in critical error: Could not find any test result files in '/tmp/xxxxx'.
-    // Creating a fake new file.
-    def file = new File("test__recon_all")
-    file.mkdir()
-
-
 }
+*/
diff --git a/tests/modules/nf-scil/segmentation/fsreconall/test.yml b/tests/modules/nf-scil/segmentation/fsreconall/test.yml
index acd1053d..7644ce82 100644
--- a/tests/modules/nf-scil/segmentation/fsreconall/test.yml
+++ b/tests/modules/nf-scil/segmentation/fsreconall/test.yml
@@ -3,5 +3,3 @@
   tags:
     - segmentation/fsreconall
     - segmentation
-  files:
-    - path: output/segmentation/versions.yml

From 3e3be0f7aed57d95a64822e5817812bac4d17db3 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Thu, 16 May 2024 17:38:40 +0000
Subject: [PATCH 09/18] Fix poetry lock

---
 poetry.lock | 31 +++++++++++--------------------
 1 file changed, 11 insertions(+), 20 deletions(-)

diff --git a/poetry.lock b/poetry.lock
index 750dd28e..6bbad418 100755
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -1330,13 +1330,13 @@ pipestatreader = ["fastapi", "uvicorn"]
 
 [[package]]
 name = "platformdirs"
-version = "4.2.1"
+version = "4.2.2"
 description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "platformdirs-4.2.1-py3-none-any.whl", hash = "sha256:17d5a1161b3fd67b390023cb2d3b026bbd40abde6fdb052dfbd3a29c3ba22ee1"},
-    {file = "platformdirs-4.2.1.tar.gz", hash = "sha256:031cd18d4ec63ec53e82dceaac0417d218a6863f7745dfcc9efe7793b7039bdf"},
+    {file = "platformdirs-4.2.2-py3-none-any.whl", hash = "sha256:2d7a1657e36a80ea911db832a8a6ece5ee53d8de21edd5cc5879af6530b1bfee"},
+    {file = "platformdirs-4.2.2.tar.gz", hash = "sha256:38b7b51f512eed9e84a22788b4bce1de17c0adb134d6becb09836e37d8654cd3"},
 ]
 
 [package.extras]
@@ -2131,22 +2131,13 @@ widechars = ["wcwidth"]
 
 [[package]]
 name = "textual"
-<<<<<<< HEAD
-version = "0.58.1"
-=======
-version = "0.59.0"
->>>>>>> 7cb01f5b83389c9353d58e83ceba98b49ae57c88
+version = "0.60.1"
 description = "Modern Text User Interface framework"
 optional = false
 python-versions = "<4.0,>=3.8"
 files = [
-<<<<<<< HEAD
-    {file = "textual-0.58.1-py3-none-any.whl", hash = "sha256:9902ebb4b00481f6fdb0e7db821c007afa45797d81e1d0651735a07de25ece87"},
-    {file = "textual-0.58.1.tar.gz", hash = "sha256:3a01be0b583f2bce38b8e9786b75ed33dddc816bba502d8e7a9ca3ca2ead3957"},
-=======
-    {file = "textual-0.59.0-py3-none-any.whl", hash = "sha256:61d6187704731a9425da0d20217a737c8738c1649c644041f868afb6963e0022"},
-    {file = "textual-0.59.0.tar.gz", hash = "sha256:0fb0001ed393a9eb2c6c8598a5436cde588658a9726b5e099ae3bfb6f3ac257d"},
->>>>>>> 7cb01f5b83389c9353d58e83ceba98b49ae57c88
+    {file = "textual-0.60.1-py3-none-any.whl", hash = "sha256:701715dfe000396c226dccaedd52fd0f56071bbdef2a1497a4f0211063ceba19"},
+    {file = "textual-0.60.1.tar.gz", hash = "sha256:258565923f55487876b48b53c1104ad660355e1853af60381ef6b10b3ed3723e"},
 ]
 
 [package.dependencies]
@@ -2351,18 +2342,18 @@ ubiquerg = ">=0.7.0"
 
 [[package]]
 name = "zipp"
-version = "3.18.1"
+version = "3.18.2"
 description = "Backport of pathlib-compatible object wrapper for zip files"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "zipp-3.18.1-py3-none-any.whl", hash = "sha256:206f5a15f2af3dbaee80769fb7dc6f249695e940acca08dfb2a4769fe61e538b"},
-    {file = "zipp-3.18.1.tar.gz", hash = "sha256:2884ed22e7d8961de1c9a05142eb69a247f120291bc0206a00a7642f09b5b715"},
+    {file = "zipp-3.18.2-py3-none-any.whl", hash = "sha256:dce197b859eb796242b0622af1b8beb0a722d52aa2f57133ead08edd5bf5374e"},
+    {file = "zipp-3.18.2.tar.gz", hash = "sha256:6278d9ddbcfb1f1089a88fde84481528b07b0e10474e09dcfe53dad4069fa059"},
 ]
 
 [package.extras]
 docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
-testing = ["big-O", "jaraco.functools", "jaraco.itertools", "more-itertools", "pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
+testing = ["big-O", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"]
 
 [[package]]
 name = "zlib-ng"

From 58a341bff0d293875f6c2e728b84a9bd87057293 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Thu, 16 May 2024 19:21:33 +0000
Subject: [PATCH 10/18] All tests pass

---
 .../segmentation/fsreconall/environment.yml   |  7 +++
 .../nf-scil/segmentation/fsreconall/main.nf   | 24 +++++---
 .../fsreconall/tests/main.nf.test             | 57 +++++++++++++++++++
 .../fsreconall/tests/main.nf.test.snap        | 14 +++++
 .../fsreconall/tests/nextflow.config          |  5 ++
 .../segmentation/fsreconall/tests/tags.yml    |  2 +
 tests/config/pytest_modules.yml               |  4 --
 .../nf-scil/segmentation/fsreconall/main.nf   | 22 -------
 .../segmentation/fsreconall/nextflow.config   |  4 --
 .../nf-scil/segmentation/fsreconall/test.yml  |  5 --
 10 files changed, 101 insertions(+), 43 deletions(-)
 create mode 100644 modules/nf-scil/segmentation/fsreconall/environment.yml
 create mode 100644 modules/nf-scil/segmentation/fsreconall/tests/main.nf.test
 create mode 100644 modules/nf-scil/segmentation/fsreconall/tests/main.nf.test.snap
 create mode 100644 modules/nf-scil/segmentation/fsreconall/tests/nextflow.config
 create mode 100644 modules/nf-scil/segmentation/fsreconall/tests/tags.yml
 delete mode 100644 tests/modules/nf-scil/segmentation/fsreconall/main.nf
 delete mode 100644 tests/modules/nf-scil/segmentation/fsreconall/nextflow.config
 delete mode 100644 tests/modules/nf-scil/segmentation/fsreconall/test.yml

diff --git a/modules/nf-scil/segmentation/fsreconall/environment.yml b/modules/nf-scil/segmentation/fsreconall/environment.yml
new file mode 100644
index 00000000..edc38fdc
--- /dev/null
+++ b/modules/nf-scil/segmentation/fsreconall/environment.yml
@@ -0,0 +1,7 @@
+---
+name: "segmentation_fsreconall"
+channels:
+  - Docker
+  - Apptainer
+dependencies:
+  - "FreeSurfer"
diff --git a/modules/nf-scil/segmentation/fsreconall/main.nf b/modules/nf-scil/segmentation/fsreconall/main.nf
index ae034c0e..84edfbd5 100644
--- a/modules/nf-scil/segmentation/fsreconall/main.nf
+++ b/modules/nf-scil/segmentation/fsreconall/main.nf
@@ -4,13 +4,13 @@ process SEGMENTATION_FSRECONALL {
 
     // Note. Freesurfer is already on Docker. See documentation on
     // https://hub.docker.com/r/freesurfer/freesurfer
-    container "freesurfer/freesurfer:7.1.1"
+    container "freesurfer/freesurfer:7.4.1"
 
     input:
         tuple val(meta), path(anat), path(fs_license) /* optional, value = [] */
 
     output:
-        path("*__recon_all")                    , emit: recon_all_out_folder
+        tuple val(meta), path("*__recon_all")   , emit: recon_all_out_folder
         path "versions.yml"                     , emit: versions
 
     when:
@@ -20,6 +20,7 @@ process SEGMENTATION_FSRECONALL {
     // Removed here.
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def dev_debug_test = task.ext.debug ? task.ext.debug : ""  // If true, we will only run the help (for unit tests )
     """
     # Manage the license. (Save old one if existed.)
     if [ $fs_license = [] ]; then
@@ -30,9 +31,16 @@ process SEGMENTATION_FSRECONALL {
         export FS_LICENSE=\$here/.license
     fi
 
-    # Run the main script
-    export SUBJECTS_DIR=`pwd`
-    recon-all -i $anat -s ${prefix}__recon_all -all
+    if [ -z $dev_debug_test ]
+    then
+        # Run the main script
+        export SUBJECTS_DIR=`pwd`
+        recon-all -i $anat -s ${prefix}__recon_all -all
+    else
+        # (for developers: unit tests: skip the long processing. help only.)
+        export SUBJECTS_DIR=`pwd`
+        recon-all -i $anat -s ${prefix}__recon_all -autorecon1 -dontrun
+    fi
 
     # Remove the license
     if [ ! $fs_license = [] ]; then
@@ -43,20 +51,20 @@ process SEGMENTATION_FSRECONALL {
     # Finish
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        freesurfer: 7.1.1
+        freesurfer: \$(recon-all -version)
     END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    recon-all -help
+    recon-all --help
 
     mkdir ${prefix}__recon_all
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        freesurfer: 7.1.1
+        freesurfer: \$(recon-all -version)
     END_VERSIONS
     """
 }
diff --git a/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test b/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test
new file mode 100644
index 00000000..622a4449
--- /dev/null
+++ b/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test
@@ -0,0 +1,57 @@
+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core modules test segmentation/fsreconall
+nextflow_process {
+
+    name "Test Process SEGMENTATION_FSRECONALL"
+    script "../main.nf"
+    process "SEGMENTATION_FSRECONALL"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "segmentation"
+    tag "segmentation/fsreconall"
+
+    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( [ "freesurfer.zip" ] )
+                input[1] = "test.load-test-data"
+                """
+            }
+        }
+    }
+
+    test("segmentation - fsreconall") {
+
+        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}/anat_image.nii.gz"),
+                        file("\${test_data_directory}/license.txt")
+                    ]}
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.recon_all_out_folder.get(0).get(1)).name
+                ).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test.snap b/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test.snap
new file mode 100644
index 00000000..c262caa7
--- /dev/null
+++ b/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test.snap
@@ -0,0 +1,14 @@
+{
+    "segmentation - fsreconall": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-16T19:18:56.050696"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-scil/segmentation/fsreconall/tests/nextflow.config b/modules/nf-scil/segmentation/fsreconall/tests/nextflow.config
new file mode 100644
index 00000000..158b50d8
--- /dev/null
+++ b/modules/nf-scil/segmentation/fsreconall/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: "SEGMENTATION_FSRECONALL" {
+        ext.debug = true
+    }
+}
diff --git a/modules/nf-scil/segmentation/fsreconall/tests/tags.yml b/modules/nf-scil/segmentation/fsreconall/tests/tags.yml
new file mode 100644
index 00000000..0035734e
--- /dev/null
+++ b/modules/nf-scil/segmentation/fsreconall/tests/tags.yml
@@ -0,0 +1,2 @@
+segmentation/fsreconall:
+  - "modules/nf-scil/segmentation/fsreconall/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 855e3825..0bc4b7f1 100755
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -13,7 +13,3 @@ testdata/scilpy:
 testdata/sizeof:
   - modules/nf-scil/testdata/sizeof/**
   - tests/modules/nf-scil/testdata/sizeof/**
-
-segmentation/fsreconall:
-  - modules/nf-scil/segmentation/fsreconall/**
-  - tests/modules/nf-scil/segmentation/fsreconall/**
diff --git a/tests/modules/nf-scil/segmentation/fsreconall/main.nf b/tests/modules/nf-scil/segmentation/fsreconall/main.nf
deleted file mode 100644
index 56c7f58d..00000000
--- a/tests/modules/nf-scil/segmentation/fsreconall/main.nf
+++ /dev/null
@@ -1,22 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { SEGMENTATION_FSRECONALL } from '../../../../../modules/nf-scil/segmentation/fsreconall/main.nf'
-
-// Too long, we don't test.
-// To test locally, add the following lines to the workflow below:
-
-/*
-workflow test_segmentation_fsreconall {
-    input = [
-        [ id:'test', single_end:false ], // meta map
-        file(params.test_data['segmentation']['fsreconall']['anat'], checkIfExists: true),
-        file(params.test_data['segmentation']['fsreconall']['license'], checkIfExists: true)
-    ]
-
-    // Hiding the real test because it is too long.
-    // SEGMENTATION_FSRECONALL ( input )
-
-}
-*/
diff --git a/tests/modules/nf-scil/segmentation/fsreconall/nextflow.config b/tests/modules/nf-scil/segmentation/fsreconall/nextflow.config
deleted file mode 100644
index 83411693..00000000
--- a/tests/modules/nf-scil/segmentation/fsreconall/nextflow.config
+++ /dev/null
@@ -1,4 +0,0 @@
-process {
-
-    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
-}
diff --git a/tests/modules/nf-scil/segmentation/fsreconall/test.yml b/tests/modules/nf-scil/segmentation/fsreconall/test.yml
deleted file mode 100644
index 7644ce82..00000000
--- a/tests/modules/nf-scil/segmentation/fsreconall/test.yml
+++ /dev/null
@@ -1,5 +0,0 @@
-- name: segmentation fsreconall test_segmentation_fsreconall
-  command: nextflow run ./tests/modules/nf-scil/segmentation/fsreconall -entry test_segmentation_fsreconall -c ./tests/config/nextflow.config
-  tags:
-    - segmentation/fsreconall
-    - segmentation

From 9bb17a0ee067f41efaad474944dd0dcc6d0bc069 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Thu, 16 May 2024 19:25:11 +0000
Subject: [PATCH 11/18] Change warning if not licence

---
 modules/nf-scil/segmentation/fsreconall/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-scil/segmentation/fsreconall/main.nf b/modules/nf-scil/segmentation/fsreconall/main.nf
index 84edfbd5..a95cc396 100644
--- a/modules/nf-scil/segmentation/fsreconall/main.nf
+++ b/modules/nf-scil/segmentation/fsreconall/main.nf
@@ -24,7 +24,7 @@ process SEGMENTATION_FSRECONALL {
     """
     # Manage the license. (Save old one if existed.)
     if [ $fs_license = [] ]; then
-        echo "License not given in input. Using default environment. "
+        echo "License not given in input. Will probably fail. "
     else
         cp $fs_license .license
         here=`pwd`

From 53a452280e80bba95d54e24940576ce79a481e81 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Thu, 16 May 2024 19:47:38 +0000
Subject: [PATCH 12/18] Remove .test_data files

---
 .test_data/betcrop/cropvolume_image.nii.gz               | 3 ---
 .test_data/betcrop/cropvolume_mask.nii.gz                | 3 ---
 .test_data/betcrop/fslbetcrop_bval.bval                  | 3 ---
 .test_data/betcrop/fslbetcrop_bvec.bvec                  | 3 ---
 .test_data/denoising/nlmeans_image.nii.gz                | 3 ---
 .test_data/denoising/nlmeans_mask.nii.gz                 | 3 ---
 .test_data/heavy/anat/anat_image.nii.gz                  | 3 ---
 .test_data/heavy/anat/anat_mask.nii.gz                   | 3 ---
 .test_data/heavy/dwi/dwi.bval                            | 3 ---
 .test_data/heavy/dwi/dwi.bvec                            | 3 ---
 .test_data/heavy/dwi/dwi.nii.gz                          | 3 ---
 .test_data/heavy/dwi/mask.nii.gz                         | 3 ---
 .test_data/heavy/dwi_with_b0/b0.nii.gz                   | 3 ---
 .test_data/heavy/dwi_with_b0/dwi.nii.gz                  | 3 ---
 .test_data/heavy/dwi_with_b0/mask.nii.gz                 | 3 ---
 .test_data/heavy/freesurfer/aparc_aseg.nii.gz            | 3 ---
 .test_data/heavy/freesurfer/license.txt                  | 3 ---
 .test_data/heavy/freesurfer/wmparc.nii.gz                | 3 ---
 .test_data/heavy/mni_152/t1_brain_probability_map.nii.gz | 3 ---
 .test_data/heavy/mni_152/t1_template.nii.gz              | 3 ---
 .test_data/light/box_3d/box_3d_image.nii.gz              | 3 ---
 .test_data/light/box_3d/box_3d_mask.nii.gz               | 3 ---
 .test_data/light/priors/s1__iso_diff.txt                 | 3 ---
 .test_data/light/priors/s1__para_diff.txt                | 3 ---
 .test_data/light/priors/s2__iso_diff.txt                 | 3 ---
 .test_data/light/priors/s2__para_diff.txt                | 3 ---
 .test_data/preproc/b0.nii.gz                             | 3 ---
 .test_data/preproc/b0_mask.nii.gz                        | 3 ---
 .test_data/preproc/dwi.nii.gz                            | 3 ---
 .test_data/preproc/dwi_normalize.nii.gz                  | 3 ---
 .test_data/preproc/dwi_normalize_bval.bval               | 3 ---
 .test_data/preproc/dwi_normalize_bvec.bvec               | 3 ---
 .test_data/preproc/dwi_normalize_mask.nii.gz             | 3 ---
 33 files changed, 99 deletions(-)
 delete mode 100755 .test_data/betcrop/cropvolume_image.nii.gz
 delete mode 100755 .test_data/betcrop/cropvolume_mask.nii.gz
 delete mode 100755 .test_data/betcrop/fslbetcrop_bval.bval
 delete mode 100755 .test_data/betcrop/fslbetcrop_bvec.bvec
 delete mode 100755 .test_data/denoising/nlmeans_image.nii.gz
 delete mode 100755 .test_data/denoising/nlmeans_mask.nii.gz
 delete mode 100755 .test_data/heavy/anat/anat_image.nii.gz
 delete mode 100755 .test_data/heavy/anat/anat_mask.nii.gz
 delete mode 100755 .test_data/heavy/dwi/dwi.bval
 delete mode 100755 .test_data/heavy/dwi/dwi.bvec
 delete mode 100755 .test_data/heavy/dwi/dwi.nii.gz
 delete mode 100755 .test_data/heavy/dwi/mask.nii.gz
 delete mode 100755 .test_data/heavy/dwi_with_b0/b0.nii.gz
 delete mode 100755 .test_data/heavy/dwi_with_b0/dwi.nii.gz
 delete mode 100755 .test_data/heavy/dwi_with_b0/mask.nii.gz
 delete mode 100755 .test_data/heavy/freesurfer/aparc_aseg.nii.gz
 delete mode 100644 .test_data/heavy/freesurfer/license.txt
 delete mode 100755 .test_data/heavy/freesurfer/wmparc.nii.gz
 delete mode 100755 .test_data/heavy/mni_152/t1_brain_probability_map.nii.gz
 delete mode 100755 .test_data/heavy/mni_152/t1_template.nii.gz
 delete mode 100755 .test_data/light/box_3d/box_3d_image.nii.gz
 delete mode 100755 .test_data/light/box_3d/box_3d_mask.nii.gz
 delete mode 100755 .test_data/light/priors/s1__iso_diff.txt
 delete mode 100755 .test_data/light/priors/s1__para_diff.txt
 delete mode 100755 .test_data/light/priors/s2__iso_diff.txt
 delete mode 100755 .test_data/light/priors/s2__para_diff.txt
 delete mode 100755 .test_data/preproc/b0.nii.gz
 delete mode 100755 .test_data/preproc/b0_mask.nii.gz
 delete mode 100755 .test_data/preproc/dwi.nii.gz
 delete mode 100755 .test_data/preproc/dwi_normalize.nii.gz
 delete mode 100755 .test_data/preproc/dwi_normalize_bval.bval
 delete mode 100755 .test_data/preproc/dwi_normalize_bvec.bvec
 delete mode 100755 .test_data/preproc/dwi_normalize_mask.nii.gz

diff --git a/.test_data/betcrop/cropvolume_image.nii.gz b/.test_data/betcrop/cropvolume_image.nii.gz
deleted file mode 100755
index e4955759..00000000
--- a/.test_data/betcrop/cropvolume_image.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:a3142e73075e193bfa45f07539502097cca1d58c68cc8b78f96db4ed1a0d3726
-size 88
diff --git a/.test_data/betcrop/cropvolume_mask.nii.gz b/.test_data/betcrop/cropvolume_mask.nii.gz
deleted file mode 100755
index 4fedac72..00000000
--- a/.test_data/betcrop/cropvolume_mask.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:a5e0db92ace8b0df83f7a50c724428517c3954c2a2c0905b6e88c847f2291461
-size 86
diff --git a/.test_data/betcrop/fslbetcrop_bval.bval b/.test_data/betcrop/fslbetcrop_bval.bval
deleted file mode 100755
index 6ca186ce..00000000
--- a/.test_data/betcrop/fslbetcrop_bval.bval
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:313d104061eeb93961146fcaa5ce5ba088e4ada652787990624bf96ad452db95
-size 1600
diff --git a/.test_data/betcrop/fslbetcrop_bvec.bvec b/.test_data/betcrop/fslbetcrop_bvec.bvec
deleted file mode 100755
index 64868a94..00000000
--- a/.test_data/betcrop/fslbetcrop_bvec.bvec
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:f54f2c4a161227e840a06a5bd39baad2977c3be6fe0804daa3fbd6b03d3e0d64
-size 4893
diff --git a/.test_data/denoising/nlmeans_image.nii.gz b/.test_data/denoising/nlmeans_image.nii.gz
deleted file mode 100755
index 6ab3d05c..00000000
--- a/.test_data/denoising/nlmeans_image.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:e5a6ed70508568b70088fdec6a9dae5d03b72907ee3132e186e944805481d908
-size 15490739
diff --git a/.test_data/denoising/nlmeans_mask.nii.gz b/.test_data/denoising/nlmeans_mask.nii.gz
deleted file mode 100755
index a9c1a35e..00000000
--- a/.test_data/denoising/nlmeans_mask.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:dcec61d61985a4d2930235e0114d0b2ab8f45ef025902cfeb346ee63ae2fdc22
-size 91555
diff --git a/.test_data/heavy/anat/anat_image.nii.gz b/.test_data/heavy/anat/anat_image.nii.gz
deleted file mode 100755
index 6ab3d05c..00000000
--- a/.test_data/heavy/anat/anat_image.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:e5a6ed70508568b70088fdec6a9dae5d03b72907ee3132e186e944805481d908
-size 15490739
diff --git a/.test_data/heavy/anat/anat_mask.nii.gz b/.test_data/heavy/anat/anat_mask.nii.gz
deleted file mode 100755
index a9c1a35e..00000000
--- a/.test_data/heavy/anat/anat_mask.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:dcec61d61985a4d2930235e0114d0b2ab8f45ef025902cfeb346ee63ae2fdc22
-size 91555
diff --git a/.test_data/heavy/dwi/dwi.bval b/.test_data/heavy/dwi/dwi.bval
deleted file mode 100755
index 6ca186ce..00000000
--- a/.test_data/heavy/dwi/dwi.bval
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:313d104061eeb93961146fcaa5ce5ba088e4ada652787990624bf96ad452db95
-size 1600
diff --git a/.test_data/heavy/dwi/dwi.bvec b/.test_data/heavy/dwi/dwi.bvec
deleted file mode 100755
index 64868a94..00000000
--- a/.test_data/heavy/dwi/dwi.bvec
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
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-size 4893
diff --git a/.test_data/heavy/dwi/dwi.nii.gz b/.test_data/heavy/dwi/dwi.nii.gz
deleted file mode 100755
index 66ebf4f8..00000000
--- a/.test_data/heavy/dwi/dwi.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:ff9205f57ccac7ff604df86ea474f4f66177293916888343f49e35e0ff81384e
-size 25156535
diff --git a/.test_data/heavy/dwi/mask.nii.gz b/.test_data/heavy/dwi/mask.nii.gz
deleted file mode 100755
index 838525be..00000000
--- a/.test_data/heavy/dwi/mask.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:b6ccd4744e6930b5f98f3f03072e03ca3c4b7290cf9627e3429f598cfa808abd
-size 19050
diff --git a/.test_data/heavy/dwi_with_b0/b0.nii.gz b/.test_data/heavy/dwi_with_b0/b0.nii.gz
deleted file mode 100755
index 6a0a4add..00000000
--- a/.test_data/heavy/dwi_with_b0/b0.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:a0aed51cc14c0f9c970c9be769db881aefe1f303dcef2a021b7abd4c4eaf5664
-size 384991
diff --git a/.test_data/heavy/dwi_with_b0/dwi.nii.gz b/.test_data/heavy/dwi_with_b0/dwi.nii.gz
deleted file mode 100755
index a2ceae40..00000000
--- a/.test_data/heavy/dwi_with_b0/dwi.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:29d36ce7920c7e1d2b63af9efb947dcb436e4477f01b5148e97644553eb8a4a9
-size 8177502
diff --git a/.test_data/heavy/dwi_with_b0/mask.nii.gz b/.test_data/heavy/dwi_with_b0/mask.nii.gz
deleted file mode 100755
index 85f42aa1..00000000
--- a/.test_data/heavy/dwi_with_b0/mask.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:f95b7fb2d1f4d793ef885df8f2ac790dfb5a71b5fef6ddd96494757d4c8a12d7
-size 6222
diff --git a/.test_data/heavy/freesurfer/aparc_aseg.nii.gz b/.test_data/heavy/freesurfer/aparc_aseg.nii.gz
deleted file mode 100755
index 7acdb4a8..00000000
--- a/.test_data/heavy/freesurfer/aparc_aseg.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
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-size 360618
diff --git a/.test_data/heavy/freesurfer/license.txt b/.test_data/heavy/freesurfer/license.txt
deleted file mode 100644
index 9c31cab4..00000000
--- a/.test_data/heavy/freesurfer/license.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:05d2a544719626968d938cca74effbd673474fdc0db1d134f77f38e2fc497f49
-size 102
diff --git a/.test_data/heavy/freesurfer/wmparc.nii.gz b/.test_data/heavy/freesurfer/wmparc.nii.gz
deleted file mode 100755
index e7108267..00000000
--- a/.test_data/heavy/freesurfer/wmparc.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
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-size 409688
diff --git a/.test_data/heavy/mni_152/t1_brain_probability_map.nii.gz b/.test_data/heavy/mni_152/t1_brain_probability_map.nii.gz
deleted file mode 100755
index ab568e81..00000000
--- a/.test_data/heavy/mni_152/t1_brain_probability_map.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
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-size 5454097
diff --git a/.test_data/heavy/mni_152/t1_template.nii.gz b/.test_data/heavy/mni_152/t1_template.nii.gz
deleted file mode 100755
index 6ab3d05c..00000000
--- a/.test_data/heavy/mni_152/t1_template.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
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-size 15490739
diff --git a/.test_data/light/box_3d/box_3d_image.nii.gz b/.test_data/light/box_3d/box_3d_image.nii.gz
deleted file mode 100755
index e4955759..00000000
--- a/.test_data/light/box_3d/box_3d_image.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
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-size 88
diff --git a/.test_data/light/box_3d/box_3d_mask.nii.gz b/.test_data/light/box_3d/box_3d_mask.nii.gz
deleted file mode 100755
index 4fedac72..00000000
--- a/.test_data/light/box_3d/box_3d_mask.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
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diff --git a/.test_data/light/priors/s1__iso_diff.txt b/.test_data/light/priors/s1__iso_diff.txt
deleted file mode 100755
index 729531b1..00000000
--- a/.test_data/light/priors/s1__iso_diff.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:98a192071ae708931f73c5daa7166c2a677bbbd4326b627b164658c8f41868d5
-size 9
diff --git a/.test_data/light/priors/s1__para_diff.txt b/.test_data/light/priors/s1__para_diff.txt
deleted file mode 100755
index f48b8eb6..00000000
--- a/.test_data/light/priors/s1__para_diff.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:5128dd18e92819bdc331bef505f1c3cb10cc2ed044a1f1e88fc44f5a52b809e9
-size 9
diff --git a/.test_data/light/priors/s2__iso_diff.txt b/.test_data/light/priors/s2__iso_diff.txt
deleted file mode 100755
index fea55c2a..00000000
--- a/.test_data/light/priors/s2__iso_diff.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:871cdcc8f4bb67480828b184c540911db878e738ec96f08f5e403d466dceab09
-size 9
diff --git a/.test_data/light/priors/s2__para_diff.txt b/.test_data/light/priors/s2__para_diff.txt
deleted file mode 100755
index 96feb91b..00000000
--- a/.test_data/light/priors/s2__para_diff.txt
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:ce38c0c5afbf0bc010dadee13130e85cf6fb7f842f7640a3af99ea3741f21cc4
-size 9
diff --git a/.test_data/preproc/b0.nii.gz b/.test_data/preproc/b0.nii.gz
deleted file mode 100755
index 6a0a4add..00000000
--- a/.test_data/preproc/b0.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:a0aed51cc14c0f9c970c9be769db881aefe1f303dcef2a021b7abd4c4eaf5664
-size 384991
diff --git a/.test_data/preproc/b0_mask.nii.gz b/.test_data/preproc/b0_mask.nii.gz
deleted file mode 100755
index 85f42aa1..00000000
--- a/.test_data/preproc/b0_mask.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:f95b7fb2d1f4d793ef885df8f2ac790dfb5a71b5fef6ddd96494757d4c8a12d7
-size 6222
diff --git a/.test_data/preproc/dwi.nii.gz b/.test_data/preproc/dwi.nii.gz
deleted file mode 100755
index a2ceae40..00000000
--- a/.test_data/preproc/dwi.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:29d36ce7920c7e1d2b63af9efb947dcb436e4477f01b5148e97644553eb8a4a9
-size 8177502
diff --git a/.test_data/preproc/dwi_normalize.nii.gz b/.test_data/preproc/dwi_normalize.nii.gz
deleted file mode 100755
index 38ffa44e..00000000
--- a/.test_data/preproc/dwi_normalize.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:008b3d3e74468e7101e0882ffe98fbcfe76b4989cb1d6860f2835d9409aee83e
-size 72960896
diff --git a/.test_data/preproc/dwi_normalize_bval.bval b/.test_data/preproc/dwi_normalize_bval.bval
deleted file mode 100755
index dfbe1d61..00000000
--- a/.test_data/preproc/dwi_normalize_bval.bval
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:155c0cab78c545a75dc71d8b1b2281d7bd17aa76e22ab0dc663171ef0e2e67bd
-size 506
diff --git a/.test_data/preproc/dwi_normalize_bvec.bvec b/.test_data/preproc/dwi_normalize_bvec.bvec
deleted file mode 100755
index 4cb7eb8a..00000000
--- a/.test_data/preproc/dwi_normalize_bvec.bvec
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:c31e57a5fc176630605fc669028ac044106d7a2cedd8e19c6dc29979f08ecf4c
-size 4631
diff --git a/.test_data/preproc/dwi_normalize_mask.nii.gz b/.test_data/preproc/dwi_normalize_mask.nii.gz
deleted file mode 100755
index 91e2bd63..00000000
--- a/.test_data/preproc/dwi_normalize_mask.nii.gz
+++ /dev/null
@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:263478c547707f405c99976dae2063bd44bb52af5c3cafac48e815a8527808a5
-size 16650

From 4b54a88e4216796dadc495d2f85b63e571024e9d Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Thu, 16 May 2024 19:49:07 +0000
Subject: [PATCH 13/18] Back to default test_data.config

---
 tests/config/test_data.config | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index 0edf1280..f34a7443 100755
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -1,7 +1,7 @@
 
 params {
     // Default endpoint provided by nf-core, we keep it here in case sometimes we end up pushing stuff to them
-    test_data_base = "https://github.com/EmmaRenauld/nf-scil/raw/module_reconall/.test_data"
+    test_data_base = "https://github.com/scilus/nf-scil/raw/main/.test_data"
     test_data {
         "image" {
             "resample" {
@@ -88,10 +88,6 @@ params {
             "fastseg" {
                 image = "${params.test_data_base}/heavy/anat/anat_image.nii.gz"
             }
-            "fsreconall" {
-                anat = "${params.test_data_base}/heavy/anat/anat_image.nii.gz"
-                license = "${params.test_data_base}/heavy/freesurfer/license.txt"
-            }
         }
         "tracking" {
             "pfttracking" {

From b0de286cf589e1557cf8c9d67ae5be51d8e0352f Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Thu, 16 May 2024 20:09:52 +0000
Subject: [PATCH 14/18] Added test that fails with no licence

---
 .../nf-scil/segmentation/fsreconall/main.nf   |  7 +++--
 .../fsreconall/tests/main.nf.test             | 31 +++++++++++++++++--
 .../fsreconall/tests/nextflow.config          |  2 +-
 .../fsreconall/tests/nextflow_debug.config    |  5 +++
 4 files changed, 39 insertions(+), 6 deletions(-)
 create mode 100644 modules/nf-scil/segmentation/fsreconall/tests/nextflow_debug.config

diff --git a/modules/nf-scil/segmentation/fsreconall/main.nf b/modules/nf-scil/segmentation/fsreconall/main.nf
index a95cc396..b14294d1 100644
--- a/modules/nf-scil/segmentation/fsreconall/main.nf
+++ b/modules/nf-scil/segmentation/fsreconall/main.nf
@@ -23,10 +23,11 @@ process SEGMENTATION_FSRECONALL {
     def dev_debug_test = task.ext.debug ? task.ext.debug : ""  // If true, we will only run the help (for unit tests )
     """
     # Manage the license. (Save old one if existed.)
-    if [ $fs_license = [] ]; then
-        echo "License not given in input. Will probably fail. "
+    if [[ ! -f "$fs_license" ]]
+    then
+        echo "License not given in input, or not found. Will probably fail. "
     else
-        cp $fs_license .license
+        cp "$fs_license" .license
         here=`pwd`
         export FS_LICENSE=\$here/.license
     fi
diff --git a/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test b/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test
index 622a4449..24d3603c 100644
--- a/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test
+++ b/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test
@@ -14,8 +14,6 @@ nextflow_process {
     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"
@@ -31,6 +29,8 @@ nextflow_process {
     test("segmentation - fsreconall") {
 
         when {
+            config "./nextflow_debug.config"
+
             process {
                 """
                 input[0] = LOAD_DATA.out.test_data_directory.map{
@@ -54,4 +54,31 @@ nextflow_process {
 
     }
 
+
+    test("segmentation - fsreconall - nolicense") {
+
+        when {
+            // Not in mode debug + no license = should fail.
+            config "./nextflow.config"
+
+            process {
+                """
+                input[0] = LOAD_DATA.out.test_data_directory.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ], // meta map
+                        file("\${test_data_directory}/anat_image.nii.gz"),
+                        []
+                    ]}
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert ! process.success }
+            )
+        }
+
+    }
+
 }
diff --git a/modules/nf-scil/segmentation/fsreconall/tests/nextflow.config b/modules/nf-scil/segmentation/fsreconall/tests/nextflow.config
index 158b50d8..4ef042e5 100644
--- a/modules/nf-scil/segmentation/fsreconall/tests/nextflow.config
+++ b/modules/nf-scil/segmentation/fsreconall/tests/nextflow.config
@@ -1,5 +1,5 @@
 process {
     withName: "SEGMENTATION_FSRECONALL" {
-        ext.debug = true
+        ext.debug = false
     }
 }
diff --git a/modules/nf-scil/segmentation/fsreconall/tests/nextflow_debug.config b/modules/nf-scil/segmentation/fsreconall/tests/nextflow_debug.config
new file mode 100644
index 00000000..158b50d8
--- /dev/null
+++ b/modules/nf-scil/segmentation/fsreconall/tests/nextflow_debug.config
@@ -0,0 +1,5 @@
+process {
+    withName: "SEGMENTATION_FSRECONALL" {
+        ext.debug = true
+    }
+}

From 9b0727dbf65f96dd20e4b9fe3560e42f5339ea45 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Thu, 16 May 2024 20:19:54 +0000
Subject: [PATCH 15/18] Remove TODO. WIP: needs to understand missing version

---
 modules/nf-scil/segmentation/fsreconall/tests/main.nf.test | 2 --
 1 file changed, 2 deletions(-)

diff --git a/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test b/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test
index 24d3603c..ef877f6c 100644
--- a/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test
+++ b/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test
@@ -1,5 +1,3 @@
-// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
-// nf-core modules test segmentation/fsreconall
 nextflow_process {
 
     name "Test Process SEGMENTATION_FSRECONALL"

From aab5140dd2af0d949d77cb00d422621c11554507 Mon Sep 17 00:00:00 2001
From: Emmanuelle <emmanuelle.renauld@usherbrooke.ca>
Date: Tue, 21 May 2024 08:34:13 -0400
Subject: [PATCH 16/18] Update
 modules/nf-scil/segmentation/fsreconall/tests/main.nf.test

Co-authored-by: Arnaud Bore <arnaud.bore@gmail.com>
---
 modules/nf-scil/segmentation/fsreconall/tests/main.nf.test | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test b/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test
index ef877f6c..dd9c3d53 100644
--- a/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test
+++ b/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test
@@ -45,7 +45,8 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    file(process.out.recon_all_out_folder.get(0).get(1)).name
+                    file(process.out.recon_all_out_folder.get(0).get(1)).name,
+                    process.out.versions
                 ).match() }
             )
         }

From 774cebc2e7385490836630dbf86ec84e369cbff2 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Tue, 21 May 2024 12:44:17 +0000
Subject: [PATCH 17/18] Tests pass!

---
 .../fsreconall/tests/main.nf.test.snap        |  5 ++-
 poetry.lock                                   | 33 +++++++++----------
 2 files changed, 20 insertions(+), 18 deletions(-)

diff --git a/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test.snap b/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test.snap
index c262caa7..f8552c23 100644
--- a/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test.snap
+++ b/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test.snap
@@ -3,12 +3,15 @@
         "content": [
             [
                 
+            ],
+            [
+                "versions.yml:md5,12027dd965b94e4d68b7e8a630a04d00"
             ]
         ],
         "meta": {
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-05-16T19:18:56.050696"
+        "timestamp": "2024-05-21T12:40:38.69571"
     }
 }
\ No newline at end of file
diff --git a/poetry.lock b/poetry.lock
index 6bbad418..a439a867 100755
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.7.1 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -1461,13 +1461,13 @@ windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "pytest"
-version = "8.2.0"
+version = "8.2.1"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "pytest-8.2.0-py3-none-any.whl", hash = "sha256:1733f0620f6cda4095bbf0d9ff8022486e91892245bb9e7d5542c018f612f233"},
-    {file = "pytest-8.2.0.tar.gz", hash = "sha256:d507d4482197eac0ba2bae2e9babf0672eb333017bcedaa5fb1a3d42c1174b3f"},
+    {file = "pytest-8.2.1-py3-none-any.whl", hash = "sha256:faccc5d332b8c3719f40283d0d44aa5cf101cec36f88cde9ed8f2bc0538612b1"},
+    {file = "pytest-8.2.1.tar.gz", hash = "sha256:5046e5b46d8e4cac199c373041f26be56fdb81eb4e67dc11d4e10811fc3408fd"},
 ]
 
 [package.dependencies]
@@ -1689,13 +1689,13 @@ yacman = ">=0.8.3"
 
 [[package]]
 name = "requests"
-version = "2.31.0"
+version = "2.32.1"
 description = "Python HTTP for Humans."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "requests-2.31.0-py3-none-any.whl", hash = "sha256:58cd2187c01e70e6e26505bca751777aa9f2ee0b7f4300988b709f44e013003f"},
-    {file = "requests-2.31.0.tar.gz", hash = "sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1"},
+    {file = "requests-2.32.1-py3-none-any.whl", hash = "sha256:21ac9465cdf8c1650fe1ecde8a71669a93d4e6f147550483a2967d08396a56a5"},
+    {file = "requests-2.32.1.tar.gz", hash = "sha256:eb97e87e64c79e64e5b8ac75cee9dd1f97f49e289b083ee6be96268930725685"},
 ]
 
 [package.dependencies]
@@ -1905,19 +1905,18 @@ files = [
 
 [[package]]
 name = "setuptools"
-version = "69.5.1"
+version = "70.0.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "setuptools-69.5.1-py3-none-any.whl", hash = "sha256:c636ac361bc47580504644275c9ad802c50415c7522212252c033bd15f301f32"},
-    {file = "setuptools-69.5.1.tar.gz", hash = "sha256:6c1fccdac05a97e598fb0ae3bbed5904ccb317337a51139dcd51453611bbb987"},
+    {file = "setuptools-70.0.0-py3-none-any.whl", hash = "sha256:54faa7f2e8d2d11bcd2c07bed282eef1046b5c080d1c32add737d7b5817b1ad4"},
+    {file = "setuptools-70.0.0.tar.gz", hash = "sha256:f211a66637b8fa059bb28183da127d4e86396c991a942b028c6650d4319c3fd0"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mypy (==1.9)", "packaging (>=23.2)", "pip (>=19.1)", "pytest (>=6,!=8.1.1)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (>=0.2.1)", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
-testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.2)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+testing = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mypy (==1.9)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.1)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (>=0.2.1)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
 name = "six"
@@ -2131,13 +2130,13 @@ widechars = ["wcwidth"]
 
 [[package]]
 name = "textual"
-version = "0.60.1"
+version = "0.62.0"
 description = "Modern Text User Interface framework"
 optional = false
 python-versions = "<4.0,>=3.8"
 files = [
-    {file = "textual-0.60.1-py3-none-any.whl", hash = "sha256:701715dfe000396c226dccaedd52fd0f56071bbdef2a1497a4f0211063ceba19"},
-    {file = "textual-0.60.1.tar.gz", hash = "sha256:258565923f55487876b48b53c1104ad660355e1853af60381ef6b10b3ed3723e"},
+    {file = "textual-0.62.0-py3-none-any.whl", hash = "sha256:5208c1df961848889ff0a0c7628f203a2bc773fc2a45d6e842b27a8e34c15499"},
+    {file = "textual-0.62.0.tar.gz", hash = "sha256:563c1c13a087c8f4fef8a47aae43e1274139e85d00e0b0898b8eb89c5e494997"},
 ]
 
 [package.dependencies]

From 36004d1907ca7ba01e741dc18581c261c1130f17 Mon Sep 17 00:00:00 2001
From: EmmaRenauld <emmanuelle.renauld@usherbrooke.ca>
Date: Tue, 21 May 2024 18:26:57 +0000
Subject: [PATCH 18/18] Update snap (and poetry) from latest test

---
 .../fsreconall/tests/main.nf.test.snap        |  8 ++---
 poetry.lock                                   | 33 +++++++++----------
 2 files changed, 19 insertions(+), 22 deletions(-)

diff --git a/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test.snap b/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test.snap
index f8552c23..45e28b9e 100644
--- a/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test.snap
+++ b/modules/nf-scil/segmentation/fsreconall/tests/main.nf.test.snap
@@ -1,9 +1,7 @@
 {
     "segmentation - fsreconall": {
         "content": [
-            [
-                
-            ],
+            "test__recon_all",
             [
                 "versions.yml:md5,12027dd965b94e4d68b7e8a630a04d00"
             ]
@@ -12,6 +10,6 @@
             "nf-test": "0.8.4",
             "nextflow": "23.10.1"
         },
-        "timestamp": "2024-05-21T12:40:38.69571"
+        "timestamp": "2024-05-21T18:19:43.835172"
     }
-}
\ No newline at end of file
+}
diff --git a/poetry.lock b/poetry.lock
index 6cc7e794..89c795f9 100755
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,4 +1,4 @@
-# This file is automatically @generated by Poetry 1.8.2 and should not be changed by hand.
+# This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
 
 [[package]]
 name = "alabaster"
@@ -1461,13 +1461,13 @@ windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "pytest"
-version = "8.2.0"
+version = "8.2.1"
 description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "pytest-8.2.0-py3-none-any.whl", hash = "sha256:1733f0620f6cda4095bbf0d9ff8022486e91892245bb9e7d5542c018f612f233"},
-    {file = "pytest-8.2.0.tar.gz", hash = "sha256:d507d4482197eac0ba2bae2e9babf0672eb333017bcedaa5fb1a3d42c1174b3f"},
+    {file = "pytest-8.2.1-py3-none-any.whl", hash = "sha256:faccc5d332b8c3719f40283d0d44aa5cf101cec36f88cde9ed8f2bc0538612b1"},
+    {file = "pytest-8.2.1.tar.gz", hash = "sha256:5046e5b46d8e4cac199c373041f26be56fdb81eb4e67dc11d4e10811fc3408fd"},
 ]
 
 [package.dependencies]
@@ -1689,13 +1689,13 @@ yacman = ">=0.8.3"
 
 [[package]]
 name = "requests"
-version = "2.31.0"
+version = "2.32.1"
 description = "Python HTTP for Humans."
 optional = false
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
-    {file = "requests-2.31.0-py3-none-any.whl", hash = "sha256:58cd2187c01e70e6e26505bca751777aa9f2ee0b7f4300988b709f44e013003f"},
-    {file = "requests-2.31.0.tar.gz", hash = "sha256:942c5a758f98d790eaed1a29cb6eefc7ffb0d1cf7af05c3d2791656dbd6ad1e1"},
+    {file = "requests-2.32.1-py3-none-any.whl", hash = "sha256:21ac9465cdf8c1650fe1ecde8a71669a93d4e6f147550483a2967d08396a56a5"},
+    {file = "requests-2.32.1.tar.gz", hash = "sha256:eb97e87e64c79e64e5b8ac75cee9dd1f97f49e289b083ee6be96268930725685"},
 ]
 
 [package.dependencies]
@@ -1905,19 +1905,18 @@ files = [
 
 [[package]]
 name = "setuptools"
-version = "69.5.1"
+version = "70.0.0"
 description = "Easily download, build, install, upgrade, and uninstall Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "setuptools-69.5.1-py3-none-any.whl", hash = "sha256:c636ac361bc47580504644275c9ad802c50415c7522212252c033bd15f301f32"},
-    {file = "setuptools-69.5.1.tar.gz", hash = "sha256:6c1fccdac05a97e598fb0ae3bbed5904ccb317337a51139dcd51453611bbb987"},
+    {file = "setuptools-70.0.0-py3-none-any.whl", hash = "sha256:54faa7f2e8d2d11bcd2c07bed282eef1046b5c080d1c32add737d7b5817b1ad4"},
+    {file = "setuptools-70.0.0.tar.gz", hash = "sha256:f211a66637b8fa059bb28183da127d4e86396c991a942b028c6650d4319c3fd0"},
 ]
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
-testing = ["build[virtualenv]", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.9)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mypy (==1.9)", "packaging (>=23.2)", "pip (>=19.1)", "pytest (>=6,!=8.1.1)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (>=0.2.1)", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
-testing-integration = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "packaging (>=23.2)", "pytest", "pytest-enabler", "pytest-xdist", "tomli", "virtualenv (>=13.0.0)", "wheel"]
+docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
+testing = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "mypy (==1.9)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.1)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (>=0.2.1)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
 
 [[package]]
 name = "six"
@@ -2131,13 +2130,13 @@ widechars = ["wcwidth"]
 
 [[package]]
 name = "textual"
-version = "0.60.1"
+version = "0.62.0"
 description = "Modern Text User Interface framework"
 optional = false
 python-versions = "<4.0,>=3.8"
 files = [
-    {file = "textual-0.60.1-py3-none-any.whl", hash = "sha256:701715dfe000396c226dccaedd52fd0f56071bbdef2a1497a4f0211063ceba19"},
-    {file = "textual-0.60.1.tar.gz", hash = "sha256:258565923f55487876b48b53c1104ad660355e1853af60381ef6b10b3ed3723e"},
+    {file = "textual-0.62.0-py3-none-any.whl", hash = "sha256:5208c1df961848889ff0a0c7628f203a2bc773fc2a45d6e842b27a8e34c15499"},
+    {file = "textual-0.62.0.tar.gz", hash = "sha256:563c1c13a087c8f4fef8a47aae43e1274139e85d00e0b0898b8eb89c5e494997"},
 ]
 
 [package.dependencies]