From bb539fded5200b031e9216ccd0364cbc0c773e01 Mon Sep 17 00:00:00 2001
From: itrujnara <itrujnara@wp.pl>
Date: Mon, 28 Oct 2024 12:18:36 +0100
Subject: [PATCH 01/11] Port check_torch_model to nf-core modules

---
 .../stimulus/checktorchmodel/environment.yml  | 17 ++++
 .../nf-core/stimulus/checktorchmodel/main.nf  | 51 ++++++++++++
 .../nf-core/stimulus/checktorchmodel/meta.yml | 80 +++++++++++++++++++
 .../checktorchmodel/tests/main.nf.test        | 68 ++++++++++++++++
 4 files changed, 216 insertions(+)
 create mode 100644 modules/nf-core/stimulus/checktorchmodel/environment.yml
 create mode 100644 modules/nf-core/stimulus/checktorchmodel/main.nf
 create mode 100644 modules/nf-core/stimulus/checktorchmodel/meta.yml
 create mode 100644 modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test

diff --git a/modules/nf-core/stimulus/checktorchmodel/environment.yml b/modules/nf-core/stimulus/checktorchmodel/environment.yml
new file mode 100644
index 00000000000..0f2a3a84635
--- /dev/null
+++ b/modules/nf-core/stimulus/checktorchmodel/environment.yml
@@ -0,0 +1,17 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - pytorch
+  - conda-forge
+  - bioconda
+dependencies:
+  - python=3.12
+  - pytorch
+  - matplotlib
+  - pandas
+  - polars
+  - ray
+  - safetensors
+  - scikit-learn
+  - pip:
+      - stimulus-py 
diff --git a/modules/nf-core/stimulus/checktorchmodel/main.nf b/modules/nf-core/stimulus/checktorchmodel/main.nf
new file mode 100644
index 00000000000..42b910a3cef
--- /dev/null
+++ b/modules/nf-core/stimulus/checktorchmodel/main.nf
@@ -0,0 +1,51 @@
+process STIMULUS_CHECKTORCHMODEL {
+    tag "$experiment_config - $original_csv"
+    label 'process_medium'
+
+    // TODO freeze to Wave
+    container "docker.io/mathysgrapotte/stimulus-py:latest"
+
+    input:
+    tuple val(meta), path(original_csv), path(experiment_config)
+    tuple val(meta2), path(model), path(ray_tune_config), path(initial_weights)
+
+    output:
+    tuple val(meta2), path("${meta.id}_${meta2.id}_modelcheck.log"), emit: log
+    path "versions.yml"                                            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    """
+    stimulus-check-model \
+        -d ${original_csv} \
+        -m ${model} \
+        -e ${experiment_config} \
+        -c ${ray_tune_config} \
+        --initial_weights ${initial_weights} \
+        --gpus ${task.accelerator.request} \
+        --cpus ${task.cpus} \
+        --memory "${task.memory}" \
+        $args > ${meta.id}_${meta2.id}_modelcheck.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Stimulus-py: \$(pip show stimulus-py | grep Version | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    """
+    touch ${meta.id}_${meta2.id}_modelcheck.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        Python: \$(python --version | cut -d ' ' -f 2)
+        Stimulus-py: \$(pip show stimulus-py | grep Version | cut -d ' ' -f 2)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/stimulus/checktorchmodel/meta.yml b/modules/nf-core/stimulus/checktorchmodel/meta.yml
new file mode 100644
index 00000000000..6674b258201
--- /dev/null
+++ b/modules/nf-core/stimulus/checktorchmodel/meta.yml
@@ -0,0 +1,80 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "stimulus_checktorchmodel"
+## TODO nf-core: Add a description of the module and list keywords
+description: Sanity check a Pytorch model using raytune
+keywords:
+  - machine learning
+  - neural network
+  - unit test
+tools:
+  - "stimulus":
+      ## TODO nf-core: Add a description and other details for the software below
+      description: "Stochastic Testing and Input Manipulation for Unbiased Learning Systems"
+      homepage: "https://github.com/mathysgrapotte/stimulus-py"
+      documentation: ""
+      tool_dev_url: "https://github.com/mathysgrapotte/stimulus-py"
+      doi: ""
+      licence: "MIT"
+      identifier: 
+
+input:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing data information
+            e.g. [ id:'test' ]
+      - original_csv:
+          type: file
+          description: A CSV file with untransformed data
+          pattern: "*.csv"
+          ontologies:
+            - edam: "http://edamontology.org/format_3752"
+      - experiment_config:
+          type: file
+          # nb will be YAML later
+          description: A JSON file describing data transformations
+          pattern: "*.json"
+          ontologies:
+            - edam: "http://edamontology.org/format_3464"
+    - - meta2:
+          type: map
+          description: |
+            Groovy Map containing model information
+            e.g. [ id:'test' ]
+      - model:
+          type: file
+          description: Python source file containing the model
+          pattern: "*.py"
+          ontologies:
+            - edam: "http://edamontology.org/format_3996"
+      - ray_tune_config:
+          type: file
+          description: YAML file containing RayTune tuning parameters
+          pattern: "*.{yaml,yml}"
+          ontologies:
+            - edam: "http://edamontology.org/format_3750"
+      - initial_weights:
+          type: file
+          description: An optional SafeTensors file containing initial weights
+          pattern: "*.safetensors"
+        
+
+output:
+  - log:
+    - "*_modelcheck.log":
+        type: file
+        description: Model check output
+        pattern: "*.log"
+  - versions:
+    - "versions.yml":
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+
+authors:
+  - "@mathysgrapotte"
+  - "@alessiovignoli"
+  - "@itrujnara"
+maintainers:
+  - "@itrujnara"
diff --git a/modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test b/modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test
new file mode 100644
index 00000000000..6f8a0f8ba59
--- /dev/null
+++ b/modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test
@@ -0,0 +1,68 @@
+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core modules test stimulus/checktorchmodel
+nextflow_process {
+
+    name "Test Process STIMULUS_CHECKTORCHMODEL"
+    script "../main.nf"
+    process "STIMULUS_CHECKTORCHMODEL"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "stimulus"
+    tag "stimulus/checktorchmodel"
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
+    test("sarscov2 - bam") {
+
+        // TODO nf-core: If you are created a test for a chained module
+        // (the module requires running more than one process to generate the required output)
+        // add the 'setup' method here.
+        // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules).
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+                
+                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+                // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples.
+            )
+        }
+
+    }
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+                
+                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+            )
+        }
+
+    }
+
+}

From 7bf66da7df6e950e30983e4fc74bd9100bb514b2 Mon Sep 17 00:00:00 2001
From: itrujnara <itrujnara@wp.pl>
Date: Mon, 28 Oct 2024 16:39:27 +0100
Subject: [PATCH 02/11] Fix stimulus/checktorchmodel structure and add nf-test

---
 .../stimulus/checktorchmodel/environment.yml  |  1 +
 .../nf-core/stimulus/checktorchmodel/main.nf  | 19 +++--
 .../nf-core/stimulus/checktorchmodel/meta.yml | 71 ++++++++-----------
 .../checktorchmodel/tests/main.nf.test        | 33 +++++----
 4 files changed, 58 insertions(+), 66 deletions(-)

diff --git a/modules/nf-core/stimulus/checktorchmodel/environment.yml b/modules/nf-core/stimulus/checktorchmodel/environment.yml
index 0f2a3a84635..b0d164429cc 100644
--- a/modules/nf-core/stimulus/checktorchmodel/environment.yml
+++ b/modules/nf-core/stimulus/checktorchmodel/environment.yml
@@ -13,5 +13,6 @@ dependencies:
   - ray
   - safetensors
   - scikit-learn
+  # NOTE https://github.com/nf-core/modules/issues/5814
   - pip:
       - stimulus-py 
diff --git a/modules/nf-core/stimulus/checktorchmodel/main.nf b/modules/nf-core/stimulus/checktorchmodel/main.nf
index 42b910a3cef..5fd491a3a0f 100644
--- a/modules/nf-core/stimulus/checktorchmodel/main.nf
+++ b/modules/nf-core/stimulus/checktorchmodel/main.nf
@@ -6,18 +6,22 @@ process STIMULUS_CHECKTORCHMODEL {
     container "docker.io/mathysgrapotte/stimulus-py:latest"
 
     input:
-    tuple val(meta), path(original_csv), path(experiment_config)
-    tuple val(meta2), path(model), path(ray_tune_config), path(initial_weights)
+    path(original_csv)
+    path(experiment_config)
+    path(model)
+    path(ray_tune_config)
+    path(initial_weights)
 
     output:
-    tuple val(meta2), path("${meta.id}_${meta2.id}_modelcheck.log"), emit: log
-    path "versions.yml"                                            , emit: versions
+    tuple val(meta), path("*_modelcheck.log"), emit: log
+    path "versions.yml"                      , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: model.replaceFirst(/\.py/, "")
     """
     stimulus-check-model \
         -d ${original_csv} \
@@ -28,7 +32,7 @@ process STIMULUS_CHECKTORCHMODEL {
         --gpus ${task.accelerator.request} \
         --cpus ${task.cpus} \
         --memory "${task.memory}" \
-        $args > ${meta.id}_${meta2.id}_modelcheck.log
+        $args > ${prefix}_modelcheck.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -39,13 +43,14 @@ process STIMULUS_CHECKTORCHMODEL {
 
     stub:
     def args = task.ext.args ?: ''
+    def STIMULUS_VER = '0.0.9' // container not used in stub, change manually
     """
-    touch ${meta.id}_${meta2.id}_modelcheck.log
+    touch ${meta.id}_modelcheck.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         Python: \$(python --version | cut -d ' ' -f 2)
-        Stimulus-py: \$(pip show stimulus-py | grep Version | cut -d ' ' -f 2)
+        Stimulus-py: ${STIMULUS_VER}
     END_VERSIONS
     """
 }
diff --git a/modules/nf-core/stimulus/checktorchmodel/meta.yml b/modules/nf-core/stimulus/checktorchmodel/meta.yml
index 6674b258201..9aa5448ef6b 100644
--- a/modules/nf-core/stimulus/checktorchmodel/meta.yml
+++ b/modules/nf-core/stimulus/checktorchmodel/meta.yml
@@ -1,7 +1,6 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "stimulus_checktorchmodel"
-## TODO nf-core: Add a description of the module and list keywords
 description: Sanity check a Pytorch model using raytune
 keywords:
   - machine learning
@@ -9,55 +8,43 @@ keywords:
   - unit test
 tools:
   - "stimulus":
-      ## TODO nf-core: Add a description and other details for the software below
       description: "Stochastic Testing and Input Manipulation for Unbiased Learning Systems"
       homepage: "https://github.com/mathysgrapotte/stimulus-py"
       documentation: ""
       tool_dev_url: "https://github.com/mathysgrapotte/stimulus-py"
       doi: ""
-      licence: "MIT"
+      licence: ["MIT"]
       identifier: 
 
 input:
-    - - meta:
-          type: map
-          description: |
-            Groovy Map containing data information
-            e.g. [ id:'test' ]
-      - original_csv:
-          type: file
-          description: A CSV file with untransformed data
-          pattern: "*.csv"
-          ontologies:
-            - edam: "http://edamontology.org/format_3752"
-      - experiment_config:
-          type: file
-          # nb will be YAML later
-          description: A JSON file describing data transformations
-          pattern: "*.json"
-          ontologies:
-            - edam: "http://edamontology.org/format_3464"
-    - - meta2:
-          type: map
-          description: |
-            Groovy Map containing model information
-            e.g. [ id:'test' ]
-      - model:
-          type: file
-          description: Python source file containing the model
-          pattern: "*.py"
-          ontologies:
-            - edam: "http://edamontology.org/format_3996"
-      - ray_tune_config:
-          type: file
-          description: YAML file containing RayTune tuning parameters
-          pattern: "*.{yaml,yml}"
-          ontologies:
-            - edam: "http://edamontology.org/format_3750"
-      - initial_weights:
-          type: file
-          description: An optional SafeTensors file containing initial weights
-          pattern: "*.safetensors"
+    - original_csv:
+        type: file
+        description: A CSV file with untransformed data
+        pattern: "*.csv"
+        ontologies:
+          - edam: "http://edamontology.org/format_3752"
+    - experiment_config:
+        type: file
+        description: A YAML file describing data transformations
+        pattern: "*.{yml,yaml}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3464"
+    - model:
+        type: file
+        description: Python source file containing the model
+        pattern: "*.py"
+        ontologies:
+          - edam: "http://edamontology.org/format_3996"
+    - ray_tune_config:
+        type: file
+        description: YAML file containing RayTune tuning parameters
+        pattern: "*.{yml,yaml}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3750"
+    - initial_weights:
+        type: file
+        description: An optional SafeTensors file containing initial weights
+        pattern: "*.safetensors"
         
 
 output:
diff --git a/modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test b/modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test
index 6f8a0f8ba59..3024239bad2 100644
--- a/modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test
+++ b/modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test
@@ -12,19 +12,16 @@ nextflow_process {
     tag "stimulus/checktorchmodel"
 
     // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
-    test("sarscov2 - bam") {
-
-        // TODO nf-core: If you are created a test for a chained module
-        // (the module requires running more than one process to generate the required output)
-        // add the 'setup' method here.
-        // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules).
+    test("basic - csv - py") {
 
         when {
             process {
                 """
-                // TODO nf-core: define inputs of the process here. Example:
-                
-                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                input[0] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/input_data_with_split.csv', checkIfExists: true),
+                input[1] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/experiment_config.yaml', checkIfExists: true),
+                input[2] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/dna_to_float_model.py', checkIfExists: true),
+                input[3] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/tune_config.yaml', checkIfExists: true),
+                input[4] = []
                 """
             }
         }
@@ -32,25 +29,28 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
-                //TODO nf-core: Add all required assertions to verify the test output.
-                // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples.
+                { with(process.out.log) {
+                    assert path(get(1)).readLines().first().contains("Trial finishes successfully")
+                } },
+                { assert snapshot(process.out.versions).match() }
             )
         }
 
     }
 
     // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
-    test("sarscov2 - bam - stub") {
+    test("basic - csv - stub") {
 
         options "-stub"
 
         when {
             process {
                 """
-                // TODO nf-core: define inputs of the process here. Example:
-                
-                input[0] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                input[0] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/input_data_with_split.csv', checkIfExists: true),
+                input[1] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/experiment_config.yaml', checkIfExists: true),
+                input[2] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/dna_to_float_model.py', checkIfExists: true),
+                input[3] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/tune_config.yaml', checkIfExists: true),
+                input[4] = []
                 """
             }
         }
@@ -59,7 +59,6 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out).match() }
-                //TODO nf-core: Add all required assertions to verify the test output.
             )
         }
 

From ad6ffdb660a3144adaf16af3760991b354c72ee6 Mon Sep 17 00:00:00 2001
From: itrujnara <itrujnara@wp.pl>
Date: Tue, 29 Oct 2024 11:56:46 +0100
Subject: [PATCH 03/11] Remove pytorch channel

---
 modules/nf-core/stimulus/checktorchmodel/environment.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/nf-core/stimulus/checktorchmodel/environment.yml b/modules/nf-core/stimulus/checktorchmodel/environment.yml
index b0d164429cc..e13b3034b9d 100644
--- a/modules/nf-core/stimulus/checktorchmodel/environment.yml
+++ b/modules/nf-core/stimulus/checktorchmodel/environment.yml
@@ -1,7 +1,6 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
-  - pytorch
   - conda-forge
   - bioconda
 dependencies:

From 9dc3eb284d1a1c080f5fcfcb4846e866cae97521 Mon Sep 17 00:00:00 2001
From: itrujnara <itrujnara@wp.pl>
Date: Tue, 29 Oct 2024 11:57:12 +0100
Subject: [PATCH 04/11] Fix initial weights parameter in
 stimulus/checktorchmodel

---
 modules/nf-core/stimulus/checktorchmodel/main.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/stimulus/checktorchmodel/main.nf b/modules/nf-core/stimulus/checktorchmodel/main.nf
index 5fd491a3a0f..f9b1a3fd82d 100644
--- a/modules/nf-core/stimulus/checktorchmodel/main.nf
+++ b/modules/nf-core/stimulus/checktorchmodel/main.nf
@@ -22,13 +22,14 @@ process STIMULUS_CHECKTORCHMODEL {
     script:
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: model.replaceFirst(/\.py/, "")
+    def weights_arg = initial_weights ? "--initial_weights ${initial_weights}" : ""
     """
     stimulus-check-model \
         -d ${original_csv} \
         -m ${model} \
         -e ${experiment_config} \
         -c ${ray_tune_config} \
-        --initial_weights ${initial_weights} \
+        ${weights_arg} \
         --gpus ${task.accelerator.request} \
         --cpus ${task.cpus} \
         --memory "${task.memory}" \

From 5ddf81bafe2fc51823047111348d75c17c5577d8 Mon Sep 17 00:00:00 2001
From: itrujnara <itrujnara@wp.pl>
Date: Tue, 29 Oct 2024 16:56:58 +0100
Subject: [PATCH 05/11] Fix stimulus/checktorchmodel tests

---
 .../stimulus/checktorchmodel/tests/main.nf.test  | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test b/modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test
index 3024239bad2..234676d0e33 100644
--- a/modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test
+++ b/modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test
@@ -17,10 +17,10 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/input_data_with_split.csv', checkIfExists: true),
-                input[1] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/experiment_config.yaml', checkIfExists: true),
-                input[2] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/dna_to_float_model.py', checkIfExists: true),
-                input[3] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/tune_config.yaml', checkIfExists: true),
+                input[0] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/input_data_with_split.csv', checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/experiment_config.yaml', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/dna_to_float_model.py', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/tune_config.yaml', checkIfExists: true)
                 input[4] = []
                 """
             }
@@ -46,10 +46,10 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/input_data_with_split.csv', checkIfExists: true),
-                input[1] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/experiment_config.yaml', checkIfExists: true),
-                input[2] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/dna_to_float_model.py', checkIfExists: true),
-                input[3] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/tune_config.yaml', checkIfExists: true),
+                input[0] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/input_data_with_split.csv', checkIfExists: true)
+                input[1] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/experiment_config.yaml', checkIfExists: true)
+                input[2] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/dna_to_float_model.py', checkIfExists: true)
+                input[3] = file(params.modules_testdata_base_path + '../../deepmodeloptim/testdata/dna_experiment/tune_config.yaml', checkIfExists: true)
                 input[4] = []
                 """
             }

From 8eeb349a1ad02cf82986aecbced9266415ed62b5 Mon Sep 17 00:00:00 2001
From: itrujnara <itrujnara@wp.pl>
Date: Tue, 29 Oct 2024 16:57:22 +0100
Subject: [PATCH 06/11] stimulus/checktorchmodel add versions to dependencies

---
 .../stimulus/checktorchmodel/environment.yml  | 22 ++++++++-----------
 1 file changed, 9 insertions(+), 13 deletions(-)

diff --git a/modules/nf-core/stimulus/checktorchmodel/environment.yml b/modules/nf-core/stimulus/checktorchmodel/environment.yml
index e13b3034b9d..fbf5fe9b102 100644
--- a/modules/nf-core/stimulus/checktorchmodel/environment.yml
+++ b/modules/nf-core/stimulus/checktorchmodel/environment.yml
@@ -1,17 +1,13 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
 channels:
   - conda-forge
   - bioconda
+
 dependencies:
-  - python=3.12
-  - pytorch
-  - matplotlib
-  - pandas
-  - polars
-  - ray
-  - safetensors
-  - scikit-learn
-  # NOTE https://github.com/nf-core/modules/issues/5814
-  - pip:
-      - stimulus-py 
+  - conda-forge::matplotlib=3.9.2
+  - conda-forge::pandas=2.2.3
+  - conda-forge::polars=1.9.0
+  - conda-forge::python=3.12
+  - conda-forge::pytorch=2.4.1
+  - conda-forge::ray-core=2.37.0
+  - conda-forge::safetensors=0.4.5
+  - conda-forge::scikit-learn=1.5.2

From fbb4798032f45d602f37e9c6dd3283e95d535ea7 Mon Sep 17 00:00:00 2001
From: itrujnara <itrujnara@wp.pl>
Date: Tue, 29 Oct 2024 16:57:39 +0100
Subject: [PATCH 07/11] stimulus/checktorchmodel fix typos in main

---
 modules/nf-core/stimulus/checktorchmodel/main.nf | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/modules/nf-core/stimulus/checktorchmodel/main.nf b/modules/nf-core/stimulus/checktorchmodel/main.nf
index f9b1a3fd82d..6a396377519 100644
--- a/modules/nf-core/stimulus/checktorchmodel/main.nf
+++ b/modules/nf-core/stimulus/checktorchmodel/main.nf
@@ -13,16 +13,17 @@ process STIMULUS_CHECKTORCHMODEL {
     path(initial_weights)
 
     output:
-    tuple val(meta), path("*_modelcheck.log"), emit: log
-    path "versions.yml"                      , emit: versions
+    path "*_modelcheck.log", emit: log
+    path "versions.yml"    , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    prefix = task.ext.prefix ?: model.replaceFirst(/\.py/, "")
+    def args        = task.ext.args ?: ''
+    prefix          = task.ext.prefix ?: model.baseName.replaceFirst(/\.py/, "")
     def weights_arg = initial_weights ? "--initial_weights ${initial_weights}" : ""
+    def gpu_arg     = task.accelerator ? "--gpus ${task.accelerator.request}" : ""
     """
     stimulus-check-model \
         -d ${original_csv} \
@@ -30,7 +31,7 @@ process STIMULUS_CHECKTORCHMODEL {
         -e ${experiment_config} \
         -c ${ray_tune_config} \
         ${weights_arg} \
-        --gpus ${task.accelerator.request} \
+        ${gpu_arg} \
         --cpus ${task.cpus} \
         --memory "${task.memory}" \
         $args > ${prefix}_modelcheck.log
@@ -43,10 +44,11 @@ process STIMULUS_CHECKTORCHMODEL {
     """
 
     stub:
-    def args = task.ext.args ?: ''
+    def args         = task.ext.args ?: ''
+    prefix           = task.ext.prefix ?: model.baseName.replaceFirst(/\.py/, "")
     def STIMULUS_VER = '0.0.9' // container not used in stub, change manually
     """
-    touch ${meta.id}_modelcheck.log
+    touch ${prefix}_modelcheck.log
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From c24b4edffa8d2907b2b16523b1e311051aa68ff8 Mon Sep 17 00:00:00 2001
From: itrujnara <itrujnara@wp.pl>
Date: Tue, 29 Oct 2024 16:57:59 +0100
Subject: [PATCH 08/11] stimulus/checktorchmodel fix typos in meta

---
 .../nf-core/stimulus/checktorchmodel/meta.yml | 60 +++++++++----------
 1 file changed, 29 insertions(+), 31 deletions(-)

diff --git a/modules/nf-core/stimulus/checktorchmodel/meta.yml b/modules/nf-core/stimulus/checktorchmodel/meta.yml
index 9aa5448ef6b..e345c6a8adc 100644
--- a/modules/nf-core/stimulus/checktorchmodel/meta.yml
+++ b/modules/nf-core/stimulus/checktorchmodel/meta.yml
@@ -10,41 +10,39 @@ tools:
   - "stimulus":
       description: "Stochastic Testing and Input Manipulation for Unbiased Learning Systems"
       homepage: "https://github.com/mathysgrapotte/stimulus-py"
-      documentation: ""
+      documentation: "https://github.com/mathysgrapotte/stimulus-py"
       tool_dev_url: "https://github.com/mathysgrapotte/stimulus-py"
-      doi: ""
       licence: ["MIT"]
-      identifier: 
 
 input:
-    - original_csv:
-        type: file
-        description: A CSV file with untransformed data
-        pattern: "*.csv"
-        ontologies:
-          - edam: "http://edamontology.org/format_3752"
-    - experiment_config:
-        type: file
-        description: A YAML file describing data transformations
-        pattern: "*.{yml,yaml}"
-        ontologies:
-          - edam: "http://edamontology.org/format_3464"
-    - model:
-        type: file
-        description: Python source file containing the model
-        pattern: "*.py"
-        ontologies:
-          - edam: "http://edamontology.org/format_3996"
-    - ray_tune_config:
-        type: file
-        description: YAML file containing RayTune tuning parameters
-        pattern: "*.{yml,yaml}"
-        ontologies:
-          - edam: "http://edamontology.org/format_3750"
-    - initial_weights:
-        type: file
-        description: An optional SafeTensors file containing initial weights
-        pattern: "*.safetensors"
+    - - original_csv:
+          type: file
+          description: A CSV file with untransformed data
+          pattern: "*.csv"
+          ontologies:
+            - edam: "http://edamontology.org/format_3752"
+    - - experiment_config:
+          type: file
+          description: A YAML file describing data transformations
+          pattern: "*.{yml,yaml}"
+          ontologies:
+            - edam: "http://edamontology.org/format_3464"
+    - - model:
+          type: file
+          description: Python source file containing the model
+          pattern: "*.py"
+          ontologies:
+            - edam: "http://edamontology.org/format_3996"
+    - - ray_tune_config:
+          type: file
+          description: YAML file containing RayTune tuning parameters
+          pattern: "*.{yml,yaml}"
+          ontologies:
+            - edam: "http://edamontology.org/format_3750"
+    - - initial_weights:
+          type: file
+          description: An optional SafeTensors file containing initial weights
+          pattern: "*.safetensors"
         
 
 output:

From 978eae76403b0c737e6f9d49989e9262e3c1aef2 Mon Sep 17 00:00:00 2001
From: itrujnara <itrujnara@wp.pl>
Date: Tue, 29 Oct 2024 16:58:12 +0100
Subject: [PATCH 09/11] stimulus/checktorchmodel run test

---
 .../checktorchmodel/tests/main.nf.test.snap   | 37 +++++++++++++++++++
 1 file changed, 37 insertions(+)
 create mode 100644 modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test.snap

diff --git a/modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test.snap b/modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test.snap
new file mode 100644
index 00000000000..9e94a8e67c4
--- /dev/null
+++ b/modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test.snap
@@ -0,0 +1,37 @@
+{
+    "basic - csv - py": {
+        "content": [
+            [
+                
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-29T15:30:33.424103"
+    },
+    "basic - csv - stub": {
+        "content": [
+            {
+                "0": [
+                    "dna_to_float_model_modelcheck.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "1": [
+                    "versions.yml:md5,673aceb3844572cdb756ae9835f9187e"
+                ],
+                "log": [
+                    "dna_to_float_model_modelcheck.log:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ],
+                "versions": [
+                    "versions.yml:md5,673aceb3844572cdb756ae9835f9187e"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-29T16:54:27.22745"
+    }
+}
\ No newline at end of file

From 1c09b33ac51b8143b7c67c81182de6978201d4f9 Mon Sep 17 00:00:00 2001
From: itrujnara <itrujnara@wp.pl>
Date: Tue, 29 Oct 2024 17:05:54 +0100
Subject: [PATCH 10/11] Make prettier happy

---
 .../nf-core/stimulus/checktorchmodel/meta.yml | 73 +++++++++----------
 1 file changed, 36 insertions(+), 37 deletions(-)

diff --git a/modules/nf-core/stimulus/checktorchmodel/meta.yml b/modules/nf-core/stimulus/checktorchmodel/meta.yml
index e345c6a8adc..c9a1274fbd5 100644
--- a/modules/nf-core/stimulus/checktorchmodel/meta.yml
+++ b/modules/nf-core/stimulus/checktorchmodel/meta.yml
@@ -15,47 +15,46 @@ tools:
       licence: ["MIT"]
 
 input:
-    - - original_csv:
-          type: file
-          description: A CSV file with untransformed data
-          pattern: "*.csv"
-          ontologies:
-            - edam: "http://edamontology.org/format_3752"
-    - - experiment_config:
-          type: file
-          description: A YAML file describing data transformations
-          pattern: "*.{yml,yaml}"
-          ontologies:
-            - edam: "http://edamontology.org/format_3464"
-    - - model:
-          type: file
-          description: Python source file containing the model
-          pattern: "*.py"
-          ontologies:
-            - edam: "http://edamontology.org/format_3996"
-    - - ray_tune_config:
-          type: file
-          description: YAML file containing RayTune tuning parameters
-          pattern: "*.{yml,yaml}"
-          ontologies:
-            - edam: "http://edamontology.org/format_3750"
-    - - initial_weights:
-          type: file
-          description: An optional SafeTensors file containing initial weights
-          pattern: "*.safetensors"
-        
+  - - original_csv:
+        type: file
+        description: A CSV file with untransformed data
+        pattern: "*.csv"
+        ontologies:
+          - edam: "http://edamontology.org/format_3752"
+  - - experiment_config:
+        type: file
+        description: A YAML file describing data transformations
+        pattern: "*.{yml,yaml}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3464"
+  - - model:
+        type: file
+        description: Python source file containing the model
+        pattern: "*.py"
+        ontologies:
+          - edam: "http://edamontology.org/format_3996"
+  - - ray_tune_config:
+        type: file
+        description: YAML file containing RayTune tuning parameters
+        pattern: "*.{yml,yaml}"
+        ontologies:
+          - edam: "http://edamontology.org/format_3750"
+  - - initial_weights:
+        type: file
+        description: An optional SafeTensors file containing initial weights
+        pattern: "*.safetensors"
 
 output:
   - log:
-    - "*_modelcheck.log":
-        type: file
-        description: Model check output
-        pattern: "*.log"
+      - "*_modelcheck.log":
+          type: file
+          description: Model check output
+          pattern: "*.log"
   - versions:
-    - "versions.yml":
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
+      - "versions.yml":
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
 
 authors:
   - "@mathysgrapotte"

From aac0a383179073cb36ed12ef50f6b5dfc4187ef8 Mon Sep 17 00:00:00 2001
From: Igor Trujnara <53370556+itrujnara@users.noreply.github.com>
Date: Wed, 30 Oct 2024 12:56:14 +0100
Subject: [PATCH 11/11] Update
 modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test

Co-authored-by: alessiovignoli <45239231+alessiovignoli@users.noreply.github.com>
---
 modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test b/modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test
index 234676d0e33..626232d8233 100644
--- a/modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test
+++ b/modules/nf-core/stimulus/checktorchmodel/tests/main.nf.test
@@ -1,4 +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 stimulus/checktorchmodel
 nextflow_process {