From 15b72c93d21fcaf7c366c6b3257ee54c9ae6352d Mon Sep 17 00:00:00 2001
From: medde <eddemanon@gmail.com>
Date: Wed, 30 Oct 2024 19:16:58 +0000
Subject: [PATCH 1/4] update reconst_fodf module

---
 modules/nf-neuro/reconst/fodf/main.nf         |  14 +-
 modules/nf-neuro/reconst/fodf/meta.yml        |   7 +-
 .../nf-neuro/reconst/fodf/tests/main.nf.test  | 220 +++++++++++-------
 .../reconst/fodf/tests/main.nf.test.snap      | 200 +++++++---------
 .../reconst/fodf/tests/nextflow_shells.config |   2 +-
 5 files changed, 231 insertions(+), 212 deletions(-)

diff --git a/modules/nf-neuro/reconst/fodf/main.nf b/modules/nf-neuro/reconst/fodf/main.nf
index 7deb635..ff5fe87 100644
--- a/modules/nf-neuro/reconst/fodf/main.nf
+++ b/modules/nf-neuro/reconst/fodf/main.nf
@@ -1,11 +1,11 @@
 
 process RECONST_FODF {
     tag "$meta.id"
-    label 'process_single'
+    label 'process_high'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://scil.usherbrooke.ca/containers/scilus_2.0.0.sif':
-        'scilus/scilus:2.0.0' }"
+        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
+        'scilus/scilus:2.0.2' }"
 
     input:
         tuple val(meta), path(dwi), path(bval), path(bvec), path(mask), path(fa), path(md), path(wm_frf), path(gm_frf), path(csf_frf)
@@ -40,7 +40,7 @@ process RECONST_FODF {
     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 set_method = task.ext.method ? task.ext.method : "ssst"
-    def processes = task.ext.processes ? "--processes " + task.ext.processes : ""
+    def processes = task.cpus > 1 ? "--processes " + task.cpus : ""
     def set_mask = mask ? "--mask $mask" : ""
     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
@@ -122,13 +122,13 @@ process RECONST_FODF {
             $set_mask $sh_basis $absolute_peaks \
             $peaks $peak_values $peak_indices \
             $afd_max $afd_total \
-            $afd_sum $nufo \
+            $afd_sum $nufo $processes \
             $relative_threshold --not_all --at \${a_threshold}
     fi
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        scilpy: 2.0.0
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
     END_VERSIONS
     """
 
@@ -159,7 +159,7 @@ process RECONST_FODF {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        scilpy: 2.0.0
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
     END_VERSIONS
     """
 }
diff --git a/modules/nf-neuro/reconst/fodf/meta.yml b/modules/nf-neuro/reconst/fodf/meta.yml
index 1f9aca2..ab3c5d7 100644
--- a/modules/nf-neuro/reconst/fodf/meta.yml
+++ b/modules/nf-neuro/reconst/fodf/meta.yml
@@ -14,7 +14,7 @@ keywords:
   - Local Model
   - Reconst
 tools:
-  - "Scilpy":
+  - "scilpy":
       description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
       homepage: "https://github.com/scilus/scilpy.git"
 
@@ -146,6 +146,11 @@ output:
       description: Number of Fiber Orientation (NuFO) map.
       pattern: "*nufo.nii.gz"
 
+  - vent_mask:
+      type: file
+      description: Ventricule mask estimated from an MD and FA threshold.
+      pattern: "*ventricles_mask.nii.gz"
+
   - versions:
       type: file
       description: File containing software versions
diff --git a/modules/nf-neuro/reconst/fodf/tests/main.nf.test b/modules/nf-neuro/reconst/fodf/tests/main.nf.test
index 76f38ec..5b9b23b 100644
--- a/modules/nf-neuro/reconst/fodf/tests/main.nf.test
+++ b/modules/nf-neuro/reconst/fodf/tests/main.nf.test
@@ -13,16 +13,22 @@ nextflow_process {
     tag "subworkflows/load_test_data"
 
     setup {
-            run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
-                script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
-                process {
-                    """
-                    input[0] = Channel.from( [ "processing.zip" , "commit_amico.zip" ] )
-                    input[1] = "test.load-test-data"
-                    """
-                }
+        run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
+            script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
+            process {
+                """
+                input[0] = Channel.from( [
+                    "DWIss2000-dir60.zip",
+                    "DWIms1000-2000-dir32-60.zip" ,
+                    "segmentation.zip",
+                    "dti.zip",
+                    "responses.zip"
+                ] )
+                input[1] = "test.load-test-data"
+                """
             }
         }
+    }
 
     test("reconst - fodf") {
 
@@ -33,23 +39,43 @@ nextflow_process {
                 """
                 ch_split_test_data = LOAD_DATA.out.test_data_directory
                     .branch{
-                        ssst: it.simpleName == "processing"
-                        msmt: it.simpleName == "commit_amico"
+                        ssst: it.simpleName == "DWIss2000-dir60"
+                        segmentation: it.simpleName == "segmentation"
+                        dti: it.simpleName == "dti"
+                        responses: it.simpleName == "responses"
                     }
-                input[0] = ch_split_test_data.ssst.map{
+                ch_dwi = ch_split_test_data.ssst.map{
                     test_data_directory -> [
-                        [ id:'test', single_end:false ],
+                        [ id:'test' ],
                         file("\${test_data_directory}/dwi.nii.gz"),
                         file("\${test_data_directory}/dwi.bval"),
-                        file("\${test_data_directory}/dwi.bvec"),
-                        file("\${test_data_directory}/cc.nii.gz"),
+                        file("\${test_data_directory}/dwi.bvec")
+                    ]
+                }
+                ch_mask = ch_split_test_data.segmentation.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/brainmask/brainmask.nii.gz")
+                    ]
+                }
+                ch_metrics = ch_split_test_data.dti.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
                         file("\${test_data_directory}/fa.nii.gz"),
-                        file("\${test_data_directory}/md.nii.gz"),
-                        file("\${test_data_directory}/frf.txt"),
-                        [],
-                        []
+                        file("\${test_data_directory}/md.nii.gz")
+                    ]
+                }
+                ch_response = ch_split_test_data.responses.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/DWIss1000-dir32.txt")
                     ]
                 }
+                input[0] = ch_dwi
+                    .join(ch_mask)
+                    .join(ch_metrics)
+                    .join(ch_response)
+                    .map{ it + [[], []] }
                 """
             }
         }
@@ -72,62 +98,43 @@ nextflow_process {
                 """
                 ch_split_test_data = LOAD_DATA.out.test_data_directory
                     .branch{
-                        ssst: it.simpleName == "processing"
-                        msmt: it.simpleName == "commit_amico"
+                        msmt: it.simpleName == "DWIms1000-2000-dir32-60"
+                        segmentation: it.simpleName == "segmentation"
+                        dti: it.simpleName == "dti"
+                        responses: it.simpleName == "responses"
                     }
-                input[0] = ch_split_test_data.ssst.map{
+                ch_dwi = ch_split_test_data.msmt.map{
                     test_data_directory -> [
-                        [ id:'test', single_end:false ],
+                        [ id:'test' ],
                         file("\${test_data_directory}/dwi.nii.gz"),
                         file("\${test_data_directory}/dwi.bval"),
-                        file("\${test_data_directory}/dwi.bvec"),
-                        file("\${test_data_directory}/cc.nii.gz"),
-                        file("\${test_data_directory}/fa.nii.gz"),
-                        file("\${test_data_directory}/md.nii.gz"),
-                        file("\${test_data_directory}/frf.txt"),
-                        [],
-                        []
+                        file("\${test_data_directory}/dwi.bvec")
                     ]
                 }
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-
-    }
-
-    test("reconst - fodf_no_mask") {
-
-        config "./nextflow.config"
-
-        when {
-            process {
-                """
-                ch_split_test_data = LOAD_DATA.out.test_data_directory
-                    .branch{
-                        ssst: it.simpleName == "processing"
-                        msmt: it.simpleName == "commit_amico"
-                    }
-                input[0] = ch_split_test_data.ssst.map{
+                ch_mask = ch_split_test_data.segmentation.map{
                     test_data_directory -> [
-                        [ id:'test', single_end:false ],
-                        file("\${test_data_directory}/dwi.nii.gz"),
-                        file("\${test_data_directory}/dwi.bval"),
-                        file("\${test_data_directory}/dwi.bvec"),
-                        [],
+                        [ id:'test' ],
+                        file("\${test_data_directory}/brainmask/brainmask.nii.gz")
+                    ]
+                }
+                ch_metrics = ch_split_test_data.dti.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
                         file("\${test_data_directory}/fa.nii.gz"),
-                        file("\${test_data_directory}/md.nii.gz"),
-                        file("\${test_data_directory}/frf.txt"),
-                        [],
-                        []
+                        file("\${test_data_directory}/md.nii.gz")
+                    ]
+                }
+                ch_response = ch_split_test_data.responses.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/DWIss1000-dir32.txt")
                     ]
                 }
+                input[0] = ch_dwi
+                    .join(ch_mask)
+                    .join(ch_metrics)
+                    .join(ch_response)
+                    .map{ it + [[], []] }
                 """
             }
         }
@@ -150,23 +157,43 @@ nextflow_process {
                 """
                 ch_split_test_data = LOAD_DATA.out.test_data_directory
                     .branch{
-                        ssst: it.simpleName == "processing"
-                        msmt: it.simpleName == "commit_amico"
+                        ssst: it.simpleName == "DWIss2000-dir60"
+                        segmentation: it.simpleName == "segmentation"
+                        dti: it.simpleName == "dti"
+                        responses: it.simpleName == "responses"
                     }
-                input[0] = ch_split_test_data.ssst.map{
+                ch_dwi = ch_split_test_data.ssst.map{
                     test_data_directory -> [
-                        [ id:'test', single_end:false ],
+                        [ id:'test' ],
                         file("\${test_data_directory}/dwi.nii.gz"),
                         file("\${test_data_directory}/dwi.bval"),
-                        file("\${test_data_directory}/dwi.bvec"),
-                        file("\${test_data_directory}/cc.nii.gz"),
+                        file("\${test_data_directory}/dwi.bvec")
+                    ]
+                }
+                ch_mask = ch_split_test_data.segmentation.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/brainmask/brainmask.nii.gz")
+                    ]
+                }
+                ch_metrics = ch_split_test_data.dti.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
                         file("\${test_data_directory}/fa.nii.gz"),
-                        file("\${test_data_directory}/md.nii.gz"),
-                        file("\${test_data_directory}/frf.txt"),
-                        [],
-                        []
+                        file("\${test_data_directory}/md.nii.gz")
+                    ]
+                }
+                ch_response = ch_split_test_data.responses.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/DWIss1000-dir32.txt")
                     ]
                 }
+                input[0] = ch_dwi
+                    .join(ch_mask)
+                    .join(ch_metrics)
+                    .join(ch_response)
+                    .map{ it + [[], []] }
                 """
             }
         }
@@ -189,24 +216,44 @@ nextflow_process {
                 """
                 ch_split_test_data = LOAD_DATA.out.test_data_directory
                     .branch{
-                        ssst: it.simpleName == "processing"
-                        msmt: it.simpleName == "commit_amico"
+                        msmt: it.simpleName == "DWIms1000-2000-dir32-60"
+                        segmentation: it.simpleName == "segmentation"
+                        dti: it.simpleName == "dti"
+                        responses: it.simpleName == "responses"
                     }
-                input[0] = ch_split_test_data.msmt.map{
+                ch_dwi = ch_split_test_data.msmt.map{
                     test_data_directory -> [
-                        [ id:'test', single_end:false ],
+                        [ id:'test' ],
                         file("\${test_data_directory}/dwi.nii.gz"),
                         file("\${test_data_directory}/dwi.bval"),
-                        file("\${test_data_directory}/dwi.bvec"),
-                        file("\${test_data_directory}/mask.nii.gz"),
+                        file("\${test_data_directory}/dwi.bvec")
+                    ]
+                }
+                ch_mask = ch_split_test_data.segmentation.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/brainmask/brainmask.nii.gz")
+                    ]
+                }
+                ch_metrics = ch_split_test_data.dti.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
                         file("\${test_data_directory}/fa.nii.gz"),
-                        file("\${test_data_directory}/md.nii.gz"),
-                        file("\${test_data_directory}/wm_frf.txt"),
-                        file("\${test_data_directory}/gm_frf.txt"),
-                        file("\${test_data_directory}/csf_frf.txt")
-
+                        file("\${test_data_directory}/md.nii.gz")
+                    ]
+                }
+                ch_response = ch_split_test_data.responses.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/DWIms1000-2000-dir32-60_wm.txt"),
+                        file("\${test_data_directory}/DWIms1000-2000-dir32-60_gm.txt"),
+                        file("\${test_data_directory}/DWIms1000-2000-dir32-60_csf.txt")
                     ]
                 }
+                input[0] = ch_dwi
+                    .join(ch_mask)
+                    .join(ch_metrics)
+                    .join(ch_response)
                 """
             }
         }
@@ -226,7 +273,8 @@ nextflow_process {
                     file(process.out.afd_max.get(0).get(1)).name,
                     file(process.out.afd_total.get(0).get(1)).name,
                     file(process.out.afd_sum.get(0).get(1)).name,
-                    file(process.out.nufo.get(0).get(1)).name).match() }
+                    file(process.out.nufo.get(0).get(1)).name,
+                    file(process.out.vent_mask.get(0).get(1)).name).match() }
             )
         }
 
diff --git a/modules/nf-neuro/reconst/fodf/tests/main.nf.test.snap b/modules/nf-neuro/reconst/fodf/tests/main.nf.test.snap
index 7c62f2a..19c210f 100644
--- a/modules/nf-neuro/reconst/fodf/tests/main.nf.test.snap
+++ b/modules/nf-neuro/reconst/fodf/tests/main.nf.test.snap
@@ -26,10 +26,9 @@
                 "0": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__fodf.nii.gz:md5,c45f0391a462d358930809502dd2da15"
+                        "test__fodf.nii.gz:md5,4ff8f1081dec638bb70fe3a12e823612"
                     ]
                 ],
                 "1": [
@@ -38,35 +37,32 @@
                 "10": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__afd_total.nii.gz:md5,9bac465d58b8662c3dce2c4937300a5a"
+                        "test__afd_total.nii.gz:md5,01a6fc27716a79cb57e1faed7ff8297b"
                     ]
                 ],
                 "11": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__afd_sum.nii.gz:md5,a849e3eb8c67cc176e88daca01669eef"
+                        "test__afd_sum.nii.gz:md5,51303ca849b1eb26b9ccd0922f33cc6a"
                     ]
                 ],
                 "12": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__nufo.nii.gz:md5,711f0ee8d01e71166099ffdf4c684b5f"
+                        "test__nufo.nii.gz:md5,458bdae89a9918b2dfc13f154bde5e1b"
                     ]
                 ],
                 "13": [
                     
                 ],
                 "14": [
-                    "versions.yml:md5,8f5a73278d63aac3bf8073c5d0ef488b"
+                    "versions.yml:md5,f80e57f2c24a4a1fd403de1d132ec6e7"
                 ],
                 "2": [
                     
@@ -83,64 +79,57 @@
                 "6": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__peaks.nii.gz:md5,fbc8af94bce991a6ebe3bfb837d39a52"
+                        "test__peaks.nii.gz:md5,e306caaad31fb77e6a068f8122651aef"
                     ]
                 ],
                 "7": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__peak_values.nii.gz:md5,4fd4a44c18544413c0e9bb672e60f709"
+                        "test__peak_values.nii.gz:md5,d65563027b11d49a0335856b924309f2"
                     ]
                 ],
                 "8": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__peak_indices.nii.gz:md5,d39ad843a7b86ac7042c44b87356e68b"
+                        "test__peak_indices.nii.gz:md5,44bb0df2cfac7efec9355b0533041f62"
                     ]
                 ],
                 "9": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__afd_max.nii.gz:md5,96b7a2dbab6306ca053b45bfad21be55"
+                        "test__afd_max.nii.gz:md5,9dbb9a0ce187b41a2a102fa3d3ca8ab7"
                     ]
                 ],
                 "afd_max": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__afd_max.nii.gz:md5,96b7a2dbab6306ca053b45bfad21be55"
+                        "test__afd_max.nii.gz:md5,9dbb9a0ce187b41a2a102fa3d3ca8ab7"
                     ]
                 ],
                 "afd_sum": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__afd_sum.nii.gz:md5,a849e3eb8c67cc176e88daca01669eef"
+                        "test__afd_sum.nii.gz:md5,51303ca849b1eb26b9ccd0922f33cc6a"
                     ]
                 ],
                 "afd_total": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__afd_total.nii.gz:md5,9bac465d58b8662c3dce2c4937300a5a"
+                        "test__afd_total.nii.gz:md5,01a6fc27716a79cb57e1faed7ff8297b"
                     ]
                 ],
                 "csf_fodf": [
@@ -149,10 +138,9 @@
                 "fodf": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__fodf.nii.gz:md5,c45f0391a462d358930809502dd2da15"
+                        "test__fodf.nii.gz:md5,4ff8f1081dec638bb70fe3a12e823612"
                     ]
                 ],
                 "gm_fodf": [
@@ -161,44 +149,40 @@
                 "nufo": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__nufo.nii.gz:md5,711f0ee8d01e71166099ffdf4c684b5f"
+                        "test__nufo.nii.gz:md5,458bdae89a9918b2dfc13f154bde5e1b"
                     ]
                 ],
                 "peak_indices": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__peak_indices.nii.gz:md5,d39ad843a7b86ac7042c44b87356e68b"
+                        "test__peak_indices.nii.gz:md5,44bb0df2cfac7efec9355b0533041f62"
                     ]
                 ],
                 "peak_values": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__peak_values.nii.gz:md5,4fd4a44c18544413c0e9bb672e60f709"
+                        "test__peak_values.nii.gz:md5,d65563027b11d49a0335856b924309f2"
                     ]
                 ],
                 "peaks": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__peaks.nii.gz:md5,fbc8af94bce991a6ebe3bfb837d39a52"
+                        "test__peaks.nii.gz:md5,e306caaad31fb77e6a068f8122651aef"
                     ]
                 ],
                 "vent_mask": [
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,8f5a73278d63aac3bf8073c5d0ef488b"
+                    "versions.yml:md5,f80e57f2c24a4a1fd403de1d132ec6e7"
                 ],
                 "vf": [
                     
@@ -212,10 +196,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-05-01T19:21:03.487368"
+        "timestamp": "2024-10-30T18:24:51.004240051"
     },
     "reconst - fodf_no_metrics": {
         "content": [
@@ -223,10 +207,9 @@
                 "0": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__fodf.nii.gz:md5,c45f0391a462d358930809502dd2da15"
+                        "test__fodf.nii.gz:md5,4ff8f1081dec638bb70fe3a12e823612"
                     ]
                 ],
                 "1": [
@@ -245,7 +228,7 @@
                     
                 ],
                 "14": [
-                    "versions.yml:md5,8f5a73278d63aac3bf8073c5d0ef488b"
+                    "versions.yml:md5,f80e57f2c24a4a1fd403de1d132ec6e7"
                 ],
                 "2": [
                     
@@ -286,10 +269,9 @@
                 "fodf": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__fodf.nii.gz:md5,c45f0391a462d358930809502dd2da15"
+                        "test__fodf.nii.gz:md5,4ff8f1081dec638bb70fe3a12e823612"
                     ]
                 ],
                 "gm_fodf": [
@@ -311,7 +293,7 @@
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,8f5a73278d63aac3bf8073c5d0ef488b"
+                    "versions.yml:md5,f80e57f2c24a4a1fd403de1d132ec6e7"
                 ],
                 "vf": [
                     
@@ -325,10 +307,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-05-01T20:22:29.171158"
+        "timestamp": "2024-10-30T18:26:49.04678007"
     },
     "reconst - fodf_with_shells": {
         "content": [
@@ -336,10 +318,9 @@
                 "0": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__fodf.nii.gz:md5,c45f0391a462d358930809502dd2da15"
+                        "test__fodf.nii.gz:md5,39a5a4a7f79ae7bfb408453887711fe2"
                     ]
                 ],
                 "1": [
@@ -348,35 +329,32 @@
                 "10": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__afd_total.nii.gz:md5,9bac465d58b8662c3dce2c4937300a5a"
+                        "test__afd_total.nii.gz:md5,31edb24c528419fcb8f6f423479e8cd9"
                     ]
                 ],
                 "11": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__afd_sum.nii.gz:md5,a849e3eb8c67cc176e88daca01669eef"
+                        "test__afd_sum.nii.gz:md5,7662527e52c86a99610bd87394b314e8"
                     ]
                 ],
                 "12": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__nufo.nii.gz:md5,711f0ee8d01e71166099ffdf4c684b5f"
+                        "test__nufo.nii.gz:md5,a8c3883e9dc99a661998d8cae6f08051"
                     ]
                 ],
                 "13": [
                     
                 ],
                 "14": [
-                    "versions.yml:md5,8f5a73278d63aac3bf8073c5d0ef488b"
+                    "versions.yml:md5,f80e57f2c24a4a1fd403de1d132ec6e7"
                 ],
                 "2": [
                     
@@ -393,64 +371,57 @@
                 "6": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__peaks.nii.gz:md5,fbc8af94bce991a6ebe3bfb837d39a52"
+                        "test__peaks.nii.gz:md5,2d4fad6ba2729dacf805aa7d056a765e"
                     ]
                 ],
                 "7": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__peak_values.nii.gz:md5,4fd4a44c18544413c0e9bb672e60f709"
+                        "test__peak_values.nii.gz:md5,5b614aae3e0b78c9ae9f7e4b85b157e3"
                     ]
                 ],
                 "8": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__peak_indices.nii.gz:md5,d39ad843a7b86ac7042c44b87356e68b"
+                        "test__peak_indices.nii.gz:md5,632878be6b5e01ad45f93553d955beeb"
                     ]
                 ],
                 "9": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__afd_max.nii.gz:md5,96b7a2dbab6306ca053b45bfad21be55"
+                        "test__afd_max.nii.gz:md5,61fb2106315ec2a20c4590b98d7e1a2c"
                     ]
                 ],
                 "afd_max": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__afd_max.nii.gz:md5,96b7a2dbab6306ca053b45bfad21be55"
+                        "test__afd_max.nii.gz:md5,61fb2106315ec2a20c4590b98d7e1a2c"
                     ]
                 ],
                 "afd_sum": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__afd_sum.nii.gz:md5,a849e3eb8c67cc176e88daca01669eef"
+                        "test__afd_sum.nii.gz:md5,7662527e52c86a99610bd87394b314e8"
                     ]
                 ],
                 "afd_total": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__afd_total.nii.gz:md5,9bac465d58b8662c3dce2c4937300a5a"
+                        "test__afd_total.nii.gz:md5,31edb24c528419fcb8f6f423479e8cd9"
                     ]
                 ],
                 "csf_fodf": [
@@ -459,10 +430,9 @@
                 "fodf": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__fodf.nii.gz:md5,c45f0391a462d358930809502dd2da15"
+                        "test__fodf.nii.gz:md5,39a5a4a7f79ae7bfb408453887711fe2"
                     ]
                 ],
                 "gm_fodf": [
@@ -471,44 +441,40 @@
                 "nufo": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__nufo.nii.gz:md5,711f0ee8d01e71166099ffdf4c684b5f"
+                        "test__nufo.nii.gz:md5,a8c3883e9dc99a661998d8cae6f08051"
                     ]
                 ],
                 "peak_indices": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__peak_indices.nii.gz:md5,d39ad843a7b86ac7042c44b87356e68b"
+                        "test__peak_indices.nii.gz:md5,632878be6b5e01ad45f93553d955beeb"
                     ]
                 ],
                 "peak_values": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__peak_values.nii.gz:md5,4fd4a44c18544413c0e9bb672e60f709"
+                        "test__peak_values.nii.gz:md5,5b614aae3e0b78c9ae9f7e4b85b157e3"
                     ]
                 ],
                 "peaks": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test__peaks.nii.gz:md5,fbc8af94bce991a6ebe3bfb837d39a52"
+                        "test__peaks.nii.gz:md5,2d4fad6ba2729dacf805aa7d056a765e"
                     ]
                 ],
                 "vent_mask": [
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,8f5a73278d63aac3bf8073c5d0ef488b"
+                    "versions.yml:md5,f80e57f2c24a4a1fd403de1d132ec6e7"
                 ],
                 "vf": [
                     
@@ -522,10 +488,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-05-01T20:38:04.916377"
+        "timestamp": "2024-10-30T18:26:01.188172837"
     },
     "reconst - fodf_no_mask": {
         "content": [
diff --git a/modules/nf-neuro/reconst/fodf/tests/nextflow_shells.config b/modules/nf-neuro/reconst/fodf/tests/nextflow_shells.config
index 791ab8c..d9bb854 100644
--- a/modules/nf-neuro/reconst/fodf/tests/nextflow_shells.config
+++ b/modules/nf-neuro/reconst/fodf/tests/nextflow_shells.config
@@ -18,6 +18,6 @@ process {
         ext.afd_total = true
         ext.afd_sum = true
         ext.nufo = true
-        ext.fodf_shells = "1000 2000 3000"
+        ext.fodf_shells = "1000 2000"
     }
 }

From 22d4e109d3b7af59df7d3386bfed5bac8ebe50e2 Mon Sep 17 00:00:00 2001
From: medde <eddemanon@gmail.com>
Date: Wed, 30 Oct 2024 19:21:49 +0000
Subject: [PATCH 2/4] update reconst_meanfrf module

---
 modules/nf-neuro/reconst/meanfrf/main.nf            | 6 +++---
 modules/nf-neuro/reconst/meanfrf/meta.yml           | 2 +-
 modules/nf-neuro/reconst/meanfrf/tests/main.nf.test | 4 ++--
 3 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/nf-neuro/reconst/meanfrf/main.nf b/modules/nf-neuro/reconst/meanfrf/main.nf
index 75c0a07..5006be5 100644
--- a/modules/nf-neuro/reconst/meanfrf/main.nf
+++ b/modules/nf-neuro/reconst/meanfrf/main.nf
@@ -8,7 +8,7 @@ process RECONST_MEANFRF {
         'scilus/scilus:2.0.2' }"
 
     input:
-        tuple path(frf_list)
+        path(frf_list)
 
     output:
         path("mean_frf.txt")                            , emit: meanfrf
@@ -27,7 +27,7 @@ process RECONST_MEANFRF {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        scilpy: 2.0.2
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
     END_VERSIONS
     """
 
@@ -39,7 +39,7 @@ process RECONST_MEANFRF {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        scilpy: 2.0.2
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
     END_VERSIONS
     """
 }
diff --git a/modules/nf-neuro/reconst/meanfrf/meta.yml b/modules/nf-neuro/reconst/meanfrf/meta.yml
index 19f5dd7..ac628bd 100644
--- a/modules/nf-neuro/reconst/meanfrf/meta.yml
+++ b/modules/nf-neuro/reconst/meanfrf/meta.yml
@@ -10,7 +10,7 @@ keywords:
   - Average
 
 tools:
-  - "Scilpy":
+  - "scilpy":
       description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
       homepage: "https://github.com/scilus/scilpy.git"
 
diff --git a/modules/nf-neuro/reconst/meanfrf/tests/main.nf.test b/modules/nf-neuro/reconst/meanfrf/tests/main.nf.test
index 8f1685c..e9f4856 100644
--- a/modules/nf-neuro/reconst/meanfrf/tests/main.nf.test
+++ b/modules/nf-neuro/reconst/meanfrf/tests/main.nf.test
@@ -31,11 +31,11 @@ nextflow_process {
             process {
                 """
                 input[0] = LOAD_DATA.out.test_data_directory
-                    .map{ test_data_directory -> [[
+                    .map{ test_data_directory -> [
                         file("\${test_data_directory}/frf.txt"),
                         file("\${test_data_directory}/mfrf.txt"),
                         file("\${test_data_directory}/nfrf.txt")
-                    ]]}
+                    ]}
                 """
             }
         }

From 43d2f895bfca7442197646466e5ca21a354f6de5 Mon Sep 17 00:00:00 2001
From: medde <eddemanon@gmail.com>
Date: Thu, 31 Oct 2024 19:57:59 +0000
Subject: [PATCH 3/4] update test modules fodf

---
 .../nf-neuro/reconst/fodf/tests/main.nf.test  |   2 +-
 .../reconst/fodf/tests/main.nf.test.snap      | 250 ++++++++++++++++--
 2 files changed, 236 insertions(+), 16 deletions(-)

diff --git a/modules/nf-neuro/reconst/fodf/tests/main.nf.test b/modules/nf-neuro/reconst/fodf/tests/main.nf.test
index 5b9b23b..9b64133 100644
--- a/modules/nf-neuro/reconst/fodf/tests/main.nf.test
+++ b/modules/nf-neuro/reconst/fodf/tests/main.nf.test
@@ -257,11 +257,11 @@ nextflow_process {
                 """
             }
         }
-
         then {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
+                    file(process.out.fodf.get(0).get(1)).name,
                     file(process.out.wm_fodf.get(0).get(1)).name,
                     file(process.out.gm_fodf.get(0).get(1)).name,
                     file(process.out.csf_fodf.get(0).get(1)).name,
diff --git a/modules/nf-neuro/reconst/fodf/tests/main.nf.test.snap b/modules/nf-neuro/reconst/fodf/tests/main.nf.test.snap
index 19c210f..a418e16 100644
--- a/modules/nf-neuro/reconst/fodf/tests/main.nf.test.snap
+++ b/modules/nf-neuro/reconst/fodf/tests/main.nf.test.snap
@@ -1,24 +1,244 @@
 {
     "reconst - fodf_msmt": {
         "content": [
-            "test__wm_fodf.nii.gz",
-            "test__gm_fodf.nii.gz",
-            "test__csf_fodf.nii.gz",
-            "test__vf.nii.gz",
-            "test__vf_rgb.nii.gz",
-            "test__peaks.nii.gz",
-            "test__peak_values.nii.gz",
-            "test__peak_indices.nii.gz",
-            "test__afd_max.nii.gz",
-            "test__afd_total.nii.gz",
-            "test__afd_sum.nii.gz",
-            "test__nufo.nii.gz"
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test__csf_fodf.nii.gz:md5,4d0f434a1bfa3ce541101c72d9e67dda",
+                            "test__fodf.nii.gz:md5,b58a2696ec28accaad8b0255bcc0a758",
+                            "test__gm_fodf.nii.gz:md5,bed2f8fcdf28852bfe87117aea67fd06",
+                            "test__wm_fodf.nii.gz:md5,b58a2696ec28accaad8b0255bcc0a758"
+                        ]
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__wm_fodf.nii.gz:md5,b58a2696ec28accaad8b0255bcc0a758"
+                    ]
+                ],
+                "10": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__afd_total.nii.gz:md5,3eaed1ef8f7904202ce23ecae07b4ffc"
+                    ]
+                ],
+                "11": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__afd_sum.nii.gz:md5,74c60aa313d05df1dd184a509e3d45b6"
+                    ]
+                ],
+                "12": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__nufo.nii.gz:md5,30080f4210d95635ed8a0126bc5ea554"
+                    ]
+                ],
+                "13": [
+                    
+                ],
+                "14": [
+                    "versions.yml:md5,f80e57f2c24a4a1fd403de1d132ec6e7"
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__gm_fodf.nii.gz:md5,bed2f8fcdf28852bfe87117aea67fd06"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__csf_fodf.nii.gz:md5,4d0f434a1bfa3ce541101c72d9e67dda"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__vf.nii.gz:md5,5909660781eb3aa6b8dae816460576c8"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__vf_rgb.nii.gz:md5,cc270c48617e814047ca33335ca67c36"
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__peaks.nii.gz:md5,a181a94b708ee8fdfb4a9cbee3fabe46"
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__peak_values.nii.gz:md5,54d55559dcc6910228c6ffb0b422ddb1"
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__peak_indices.nii.gz:md5,4f134a0f0a6f0b1c55365d4f9569b42e"
+                    ]
+                ],
+                "9": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__afd_max.nii.gz:md5,4d0482ab9f57b0869cd13e1c8ad150ae"
+                    ]
+                ],
+                "afd_max": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__afd_max.nii.gz:md5,4d0482ab9f57b0869cd13e1c8ad150ae"
+                    ]
+                ],
+                "afd_sum": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__afd_sum.nii.gz:md5,74c60aa313d05df1dd184a509e3d45b6"
+                    ]
+                ],
+                "afd_total": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__afd_total.nii.gz:md5,3eaed1ef8f7904202ce23ecae07b4ffc"
+                    ]
+                ],
+                "csf_fodf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__csf_fodf.nii.gz:md5,4d0f434a1bfa3ce541101c72d9e67dda"
+                    ]
+                ],
+                "fodf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test__csf_fodf.nii.gz:md5,4d0f434a1bfa3ce541101c72d9e67dda",
+                            "test__fodf.nii.gz:md5,b58a2696ec28accaad8b0255bcc0a758",
+                            "test__gm_fodf.nii.gz:md5,bed2f8fcdf28852bfe87117aea67fd06",
+                            "test__wm_fodf.nii.gz:md5,b58a2696ec28accaad8b0255bcc0a758"
+                        ]
+                    ]
+                ],
+                "gm_fodf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__gm_fodf.nii.gz:md5,bed2f8fcdf28852bfe87117aea67fd06"
+                    ]
+                ],
+                "nufo": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__nufo.nii.gz:md5,30080f4210d95635ed8a0126bc5ea554"
+                    ]
+                ],
+                "peak_indices": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__peak_indices.nii.gz:md5,4f134a0f0a6f0b1c55365d4f9569b42e"
+                    ]
+                ],
+                "peak_values": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__peak_values.nii.gz:md5,54d55559dcc6910228c6ffb0b422ddb1"
+                    ]
+                ],
+                "peaks": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__peaks.nii.gz:md5,a181a94b708ee8fdfb4a9cbee3fabe46"
+                    ]
+                ],
+                "vent_mask": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,f80e57f2c24a4a1fd403de1d132ec6e7"
+                ],
+                "vf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__vf.nii.gz:md5,5909660781eb3aa6b8dae816460576c8"
+                    ]
+                ],
+                "vf_rgb": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__vf_rgb.nii.gz:md5,cc270c48617e814047ca33335ca67c36"
+                    ]
+                ],
+                "wm_fodf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__wm_fodf.nii.gz:md5,b58a2696ec28accaad8b0255bcc0a758"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
         },
-        "timestamp": "2024-05-07T17:04:27.988184"
+        "timestamp": "2024-10-31T15:39:37.96014247"
     },
     "reconst - fodf": {
         "content": [

From f609d8e850e71779e12409fada0f976d07a3efb8 Mon Sep 17 00:00:00 2001
From: medde <eddemanon@gmail.com>
Date: Thu, 31 Oct 2024 20:00:00 +0000
Subject: [PATCH 4/4] update test modules fodf add version

---
 modules/nf-neuro/reconst/fodf/tests/main.nf.test | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/nf-neuro/reconst/fodf/tests/main.nf.test b/modules/nf-neuro/reconst/fodf/tests/main.nf.test
index 9b64133..5827248 100644
--- a/modules/nf-neuro/reconst/fodf/tests/main.nf.test
+++ b/modules/nf-neuro/reconst/fodf/tests/main.nf.test
@@ -274,7 +274,8 @@ nextflow_process {
                     file(process.out.afd_total.get(0).get(1)).name,
                     file(process.out.afd_sum.get(0).get(1)).name,
                     file(process.out.nufo.get(0).get(1)).name,
-                    file(process.out.vent_mask.get(0).get(1)).name).match() }
+                    file(process.out.vent_mask.get(0).get(1)).name,
+                    file(process.out.versions.get(0).get(1)).name).match() }
             )
         }