added test with multiple subjects + update more modules with patch fi…

…les.
scilus · Dec 28, 2024 · e779d08 · e779d08
1 parent 7f3df8c
commit e779d08
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Showing 20 changed files with 955 additions and 152 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -40,6 +40,7 @@ jobs:
           - "connectomics.nf.test"
           - "tracking.nf.test"
           - "freesurfer.nf.test"
+          - "multisubjects.nf.test"
         isMaster:
           - ${{ github.base_ref == 'master' }}
         # Exclude conda and singularity on dev

diff --git a/modules.json b/modules.json
diff --git a/modules/nf-neuro/betcrop/synthbet/betcrop-synthbet.diff b/modules/nf-neuro/betcrop/synthbet/betcrop-synthbet.diff
@@ -1,18 +1,39 @@
-Changes in module 'nf-neuro/betcrop/synthbet'
+Changes in component 'nf-neuro/betcrop/synthbet'
 'modules/nf-neuro/betcrop/synthbet/environment.yml' is unchanged
 'modules/nf-neuro/betcrop/synthbet/meta.yml' is unchanged
 Changes in 'betcrop/synthbet/main.nf':
 --- modules/nf-neuro/betcrop/synthbet/main.nf
 +++ modules/nf-neuro/betcrop/synthbet/main.nf
-@@ -40,7 +40,7 @@
-     def prefix = task.ext.prefix ?: "${meta.id}"
+@@ -2,7 +2,10 @@
+     tag "$meta.id"
+     label 'process_single'
 
+-    container "freesurfer/freesurfer:7.4.1"
++    container "freesurfer/synthstrip:1.5"
++    containerOptions {
++        (workflow.containerEngine == 'docker') ? '--entrypoint ""': ''
++    }
+
+     input:
+     tuple val(meta), path(image), path(weights) /* optional, input = [] */
+@@ -32,7 +35,7 @@
+
+     cat <<-END_VERSIONS > versions.yml
+     "${task.process}":
+-        Freesurfer: \$(mri_convert -version | grep "freesurfer" | sed -E 's/.* ([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/')
++        synthstrip: 1.5
+     END_VERSIONS
      """
--    mri_synthstrip -h
-+    #mri_synthstrip -h
 
-     touch ${prefix}__bet_image.nii.gz
-     touch ${prefix}__brain_mask.nii.gz
+@@ -45,7 +48,7 @@
+
+     cat <<-END_VERSIONS > versions.yml
+     "${task.process}":
+-        Freesurfer: \$(mri_convert -version | grep "freesurfer" | sed -E 's/.* ([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/')
++        synthstrip: 1.5
+     END_VERSIONS
+
+     function handle_code () {
 
 'modules/nf-neuro/betcrop/synthbet/tests/main.nf.test.snap' is unchanged
 'modules/nf-neuro/betcrop/synthbet/tests/tags.yml' is unchanged

diff --git a/modules/nf-neuro/betcrop/synthbet/main.nf b/modules/nf-neuro/betcrop/synthbet/main.nf
@@ -2,7 +2,10 @@ process BETCROP_SYNTHBET {
     tag "$meta.id"
     label 'process_single'
 
-    container "freesurfer/freesurfer:7.4.1"
+    container "freesurfer/synthstrip:1.5"
+    containerOptions {
+        (workflow.containerEngine == 'docker') ? '--entrypoint ""': ''
+    }
 
     input:
     tuple val(meta), path(image), path(weights) /* optional, input = [] */
@@ -32,7 +35,7 @@ process BETCROP_SYNTHBET {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        Freesurfer: \$(mri_convert -version | grep "freesurfer" | sed -E 's/.* ([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/')
+        synthstrip: 1.5
     END_VERSIONS
     """
 
@@ -45,7 +48,7 @@ process BETCROP_SYNTHBET {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        Freesurfer: \$(mri_convert -version | grep "freesurfer" | sed -E 's/.* ([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/')
+        synthstrip: 1.5
     END_VERSIONS
 
     function handle_code () {

diff --git a/modules/nf-neuro/preproc/eddy/main.nf b/modules/nf-neuro/preproc/eddy/main.nf
@@ -114,32 +114,36 @@ process PREPROC_EDDY {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    scil_volume_math.py -h
-    #maskfilter -h
-    #bet -h
-    scil_dwi_extract_b0.py -h
-    scil_gradients_validate_correct_eddy.py -h
-    scil_dwi_concatenate.py -h
-    mrconvert -h
-    scil_dwi_prepare_eddy_command.py -h
-    scil_header_print_info.py -h
-
     touch ${prefix}__dwi_corrected.nii.gz
     touch ${prefix}__dwi_eddy_corrected.bval
     touch ${prefix}__dwi_eddy_corrected.bvec
     touch ${prefix}__b0_bet_mask.nii.gz
 
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
         mrtrix: \$(dwidenoise -version 2>&1 | sed -n 's/== dwidenoise \\([0-9.]\\+\\).*/\\1/p')
         fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')
-
     END_VERSIONS
+
+    function handle_code () {
+    local code=\$?
+    ignore=( 1 )
+    exit \$([[ " \${ignore[@]} " =~ " \$code " ]] && echo 0 || echo \$code)
+    }
+    trap 'handle_code' ERR
+
+    scil_volume_math.py -h
+    maskfilter -h
+    bet -h
+    scil_dwi_extract_b0.py -h
+    scil_gradients_validate_correct_eddy.py -h
+    scil_dwi_concatenate.py -h
+    mrconvert -h
+    scil_dwi_prepare_eddy_command.py -h
+    scil_header_print_info.py -h
     """
 }
diff --git a/modules/nf-neuro/preproc/eddy/preproc-eddy.diff b/modules/nf-neuro/preproc/eddy/preproc-eddy.diff
@@ -1,20 +1,20 @@
-Changes in module 'nf-neuro/preproc/eddy'
+Changes in component 'nf-neuro/preproc/eddy'
 'modules/nf-neuro/preproc/eddy/environment.yml' is unchanged
 'modules/nf-neuro/preproc/eddy/meta.yml' is unchanged
 Changes in 'preproc/eddy/main.nf':
 --- modules/nf-neuro/preproc/eddy/main.nf
 +++ modules/nf-neuro/preproc/eddy/main.nf
-@@ -119,8 +119,8 @@
+@@ -3,8 +3,8 @@
+     label 'process_high'
 
-     """
-     scil_volume_math.py -h
--    maskfilter -h
--    bet -h
-+    #maskfilter -h
-+    #bet -h
-     scil_dwi_extract_b0.py -h
-     scil_gradients_validate_correct_eddy.py -h
-     scil_dwi_concatenate.py -h
+     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+-        "https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif":
+-        "scilus/scilus:2.0.2"}"
++        '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(rev_dwi), path(rev_bval), path(rev_bvec), path(corrected_b0s), path(topup_fieldcoef), path(topup_movpart)
 
 'modules/nf-neuro/preproc/eddy/tests/main.nf.test.snap' is unchanged
 'modules/nf-neuro/preproc/eddy/tests/tags.yml' is unchanged

diff --git a/modules/nf-neuro/preproc/eddy/tests/main.nf.test b/modules/nf-neuro/preproc/eddy/tests/main.nf.test
@@ -93,4 +93,34 @@ nextflow_process {
             )
         }
     }
+
+    test("eddy - stub-run") {
+        options "-stub-run"
+        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}/sub-01_dir-AP_dwi.nii.gz", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-AP_dwi.bval", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-AP_dwi.bvec", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-PA_dwi.nii.gz", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-PA_dwi.bval", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-PA_dwi.bvec", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01__corrected_b0s.nii.gz", checkIfExists: true),
+                    file("\${test_data_directory}/topup_results_fieldcoef.nii.gz", checkIfExists: true),
+                    file("\${test_data_directory}/topup_results_movpar.txt", checkIfExists: true)
+                    ]
+                }
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-neuro/preproc/eddy/tests/main.nf.test.snap b/modules/nf-neuro/preproc/eddy/tests/main.nf.test.snap
@@ -62,5 +62,17 @@
             "nextflow": "24.04.4"
         },
         "timestamp": "2024-11-21T19:53:14.315721034"
+    },
+    "eddy - stub-run": {
+        "content": [
+            [
+                "versions.yml:md5,137e3ce0fd25e5b16de2d8cc5a5aefca"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-12-12T12:50:30.654366"
     }
 }
diff --git a/modules/nf-neuro/preproc/topup/main.nf b/modules/nf-neuro/preproc/topup/main.nf
@@ -8,7 +8,7 @@ process PREPROC_TOPUP {
 
     input:
         tuple val(meta), path(dwi), path(bval), path(bvec), path(b0), path(rev_dwi), path(rev_bval), path(rev_bvec), path(rev_b0)
-        val(config_topup)
+        each config_topup
 
     output:
         tuple val(meta), path("*__corrected_b0s.nii.gz"), emit: topup_corrected_b0s
@@ -73,16 +73,10 @@ process PREPROC_TOPUP {
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     def prefix_topup = task.ext.prefix_topup ? task.ext.prefix_topup : ""
 
     """
-    scil_volume_math.py -h
-    scil_dwi_extract_b0.py -h
-    #antsRegistrationSyNQuick.sh
-    scil_dwi_prepare_topup_command.py -h
-
     touch ${prefix}__corrected_b0s.nii.gz
     touch ${prefix}__rev_b0_warped.nii.gz
     touch ${prefix}__rev_b0_mean.nii.gz
@@ -95,7 +89,18 @@ process PREPROC_TOPUP {
         scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
         antsRegistration: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\+\\).*/\\1/')
         fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')
-
     END_VERSIONS
+
+    function handle_code () {
+    local code=\$?
+    ignore=( 1 )
+    exit \$([[ " \${ignore[@]} " =~ " \$code " ]] && echo 0 || echo \$code)
+    }
+    trap 'handle_code' ERR
+
+    scil_volume_math.py -h
+    scil_dwi_extract_b0.py -h
+    antsRegistrationSyNQuick.sh
+    scil_dwi_prepare_topup_command.py -h
     """
 }
diff --git a/modules/nf-neuro/preproc/topup/preproc-topup.diff b/modules/nf-neuro/preproc/topup/preproc-topup.diff
@@ -1,18 +1,25 @@
-Changes in module 'nf-neuro/preproc/topup'
+Changes in component 'nf-neuro/preproc/topup'
 'modules/nf-neuro/preproc/topup/environment.yml' is unchanged
 'modules/nf-neuro/preproc/topup/meta.yml' is unchanged
 Changes in 'preproc/topup/main.nf':
 --- modules/nf-neuro/preproc/topup/main.nf
 +++ modules/nf-neuro/preproc/topup/main.nf
-@@ -80,7 +80,7 @@
-     """
-     scil_volume_math.py -h
-     scil_dwi_extract_b0.py -h
--    antsRegistrationSyNQuick.sh -h
-+    #antsRegistrationSyNQuick.sh
-     scil_dwi_prepare_topup_command.py -h
+@@ -3,12 +3,12 @@
+     label 'process_single'
 
-     touch ${prefix}__corrected_b0s.nii.gz
+     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+-        "https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif":
+-        "scilus/scilus:2.0.2"}"
++        '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(b0), path(rev_dwi), path(rev_bval), path(rev_bvec), path(rev_b0)
+-        val(config_topup)
++        each config_topup
+
+     output:
+         tuple val(meta), path("*__corrected_b0s.nii.gz"), emit: topup_corrected_b0s
 
 'modules/nf-neuro/preproc/topup/tests/main.nf.test.snap' is unchanged
 'modules/nf-neuro/preproc/topup/tests/tags.yml' is unchanged

diff --git a/modules/nf-neuro/preproc/topup/tests/main.nf.test b/modules/nf-neuro/preproc/topup/tests/main.nf.test
@@ -95,4 +95,32 @@ nextflow_process {
             )
         }
     }
+
+    test("topup - stub-run") {
+        options "-stub-run"
+        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}/sub-01_dir-AP_dwi.nii.gz", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-AP_dwi.bval", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-AP_dwi.bvec", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-AP_sbref.nii.gz", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-PA_dwi.nii.gz", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-PA_dwi.bval", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-PA_dwi.bvec", checkIfExists: true),
+                    file("\${test_data_directory}/sub-01_dir-PA_sbref.nii.gz", checkIfExists: true)]}
+                input[1] = []
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
 }
diff --git a/modules/nf-neuro/preproc/topup/tests/main.nf.test.snap b/modules/nf-neuro/preproc/topup/tests/main.nf.test.snap
@@ -33,6 +33,18 @@
         },
         "timestamp": "2024-11-01T16:21:18.752887499"
     },
+    "topup - stub-run": {
+        "content": [
+            [
+                "versions.yml:md5,1e46217f093e27a6a26cd479f074296b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-12-12T11:56:01.860981"
+    },
     "topup_light": {
         "content": [
             "test__corrected_b0s.nii.gz",

diff --git a/subworkflows/nf-core/utils_nfcore_pipeline/main.nf b/subworkflows/nf-core/utils_nfcore_pipeline/main.nf