From 9f6990680a533e7ceef3b1fe776332f78cd14d95 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Kre=C5=A1imir=20Be=C5=A1tak?=
 <86408271+kbestak@users.noreply.github.com>
Date: Wed, 20 Mar 2024 13:13:32 +0100
Subject: [PATCH] Added contrast limited adaptive histogram equalization module
 (#5268)

* clahe_module

* removed todos

* Fixed linting, excluded conda tests.

* Added conda test skip to workflows/test.yml.

---------

Co-authored-by: Florian Wuennemann <flowuenne@gmail.com>
---
 .github/workflows/test.yml                    |  2 +
 modules/nf-core/molkartgarage/clahe/main.nf   | 49 +++++++++++++++
 modules/nf-core/molkartgarage/clahe/meta.yml  | 52 ++++++++++++++++
 .../molkartgarage/clahe/tests/main.nf.test    | 60 +++++++++++++++++++
 .../clahe/tests/main.nf.test.snap             | 14 +++++
 .../molkartgarage/clahe/tests/nextflow.config |  7 +++
 .../molkartgarage/clahe/tests/tags.yml        |  2 +
 7 files changed, 186 insertions(+)
 create mode 100644 modules/nf-core/molkartgarage/clahe/main.nf
 create mode 100644 modules/nf-core/molkartgarage/clahe/meta.yml
 create mode 100644 modules/nf-core/molkartgarage/clahe/tests/main.nf.test
 create mode 100644 modules/nf-core/molkartgarage/clahe/tests/main.nf.test.snap
 create mode 100644 modules/nf-core/molkartgarage/clahe/tests/nextflow.config
 create mode 100644 modules/nf-core/molkartgarage/clahe/tests/tags.yml

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
index 544b2cf26b1..6bf82516a05 100644
--- a/.github/workflows/test.yml
+++ b/.github/workflows/test.yml
@@ -561,6 +561,8 @@ jobs:
             tags: merquryfk/merquryfk
           - profile: conda
             tags: merquryfk/ploidyplot
+          - profile: conda
+            tags: molkartgarage/clahe
           - profile: conda
             tags: quartonotebook
           - profile: conda
diff --git a/modules/nf-core/molkartgarage/clahe/main.nf b/modules/nf-core/molkartgarage/clahe/main.nf
new file mode 100644
index 00000000000..1d070aeebcf
--- /dev/null
+++ b/modules/nf-core/molkartgarage/clahe/main.nf
@@ -0,0 +1,49 @@
+process MOLKARTGARAGE_CLAHE {
+    tag "$meta.id"
+    label 'process_medium'
+
+    container "ghcr.io/schapirolabor/molkart-local:v0.1.1"
+
+    input:
+    tuple val(meta), path(image)
+
+    output:
+    tuple val(meta), path("*.tiff") , emit: img_clahe
+    path "versions.yml"             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "Molkartgarage/clahe module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def args   = task.ext.args   ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    python /local/scripts/molkart_clahe.py \
+        --input ${image} \
+        --output ${prefix}.tiff \
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        molkart_clahe: \$(python /local/scripts/molkart_clahe.py --version)
+        scikit-image: 0.19.2
+    END_VERSIONS
+    """
+
+    stub:
+    def args   = task.ext.args   ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.tiff
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        molkart_clahe: \$(python3 /local/scripts/molkart_clahe.py  --version)
+        scikit-image: 0.19.2
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/molkartgarage/clahe/meta.yml b/modules/nf-core/molkartgarage/clahe/meta.yml
new file mode 100644
index 00000000000..9ca71304aa3
--- /dev/null
+++ b/modules/nf-core/molkartgarage/clahe/meta.yml
@@ -0,0 +1,52 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "molkartgarage_clahe"
+description: Contrast-limited adjusted histogram equalization (CLAHE) on single-channel tif images.
+keywords:
+  - clahe
+  - image_processing
+  - imaging
+  - correction
+tools:
+  - "molkartgarage":
+      description: "One-stop-shop for scripts and tools for processing data for molkart and spatial omics pipelines."
+      homepage: https://github.com/SchapiroLabor/molkart-local/tree/main
+      documentation: https://github.com/SchapiroLabor/molkart-local/tree/main
+      tool_dev_url: https://github.com/SchapiroLabor/molkart-local/blob/main/scripts/molkart_clahe.py
+      licence: ["MIT"]
+
+input:
+  # Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1']`
+
+  - image:
+      type: file
+      description: Single-channel tiff file to be corrected.
+      pattern: "*.{tif,tiff}"
+
+output:
+  #Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1']`
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+  - img_clahe:
+      type: file
+      description: CLAHE corrected tiff file.
+      pattern: "*.{tiff}"
+
+authors:
+  - "@kbestak"
+maintainers:
+  - "@kbestak"
diff --git a/modules/nf-core/molkartgarage/clahe/tests/main.nf.test b/modules/nf-core/molkartgarage/clahe/tests/main.nf.test
new file mode 100644
index 00000000000..15c67b7d7fa
--- /dev/null
+++ b/modules/nf-core/molkartgarage/clahe/tests/main.nf.test
@@ -0,0 +1,60 @@
+// test with: nf-core modules test molkartgarage/clahe
+nextflow_process {
+
+    name "Test Process MOLKARTGARAGE_CLAHE"
+    script "../main.nf"
+    config "./nextflow.config"
+    process "MOLKARTGARAGE_CLAHE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "molkartgarage"
+    tag "molkartgarage/clahe"
+
+    test("clahe - tiff") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['imaging']['tiff']['mouse_heart_wga'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.img_clahe }, // uuid in metadata changes so md5sums are not the same
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+
+    }
+
+    test("clahe - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['imaging']['tiff']['mouse_heart_wga'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/molkartgarage/clahe/tests/main.nf.test.snap b/modules/nf-core/molkartgarage/clahe/tests/main.nf.test.snap
new file mode 100644
index 00000000000..349a0e9bfa6
--- /dev/null
+++ b/modules/nf-core/molkartgarage/clahe/tests/main.nf.test.snap
@@ -0,0 +1,14 @@
+{
+    "versions": {
+        "content": [
+            [
+                "versions.yml:md5,ddf084b777e987eb83271f02e4e4cf2b"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-03-19T13:20:00.607838647"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/molkartgarage/clahe/tests/nextflow.config b/modules/nf-core/molkartgarage/clahe/tests/nextflow.config
new file mode 100644
index 00000000000..72dd3fcceec
--- /dev/null
+++ b/modules/nf-core/molkartgarage/clahe/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+
+    withName: "MOLKARTGARAGE_CLAHE" {
+        ext.args = '--tile-size 368 --tile-size 48 --pixel-size 0.138 --cliplimit 0.01'
+    }
+
+}
diff --git a/modules/nf-core/molkartgarage/clahe/tests/tags.yml b/modules/nf-core/molkartgarage/clahe/tests/tags.yml
new file mode 100644
index 00000000000..b7bba012974
--- /dev/null
+++ b/modules/nf-core/molkartgarage/clahe/tests/tags.yml
@@ -0,0 +1,2 @@
+molkartgarage/clahe:
+  - "modules/nf-core/molkartgarage/clahe/**"