nf-core wrapper module for harmonise_xenium.py (nf_xenium_feature_extraction)

modules/sanger-cellgeni/ml/xeniumharmonise/environment.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "YOUR-TOOL-HERE"

modules/sanger-cellgeni/ml/xeniumharmonise/main.nf

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+
+process ML_XENIUMHARMONISE {
+    tag "$meta"
+
+    container '/nfs/cellgeni/singularity/images/palom_tiledb.sif'
+
+
+    input:
+    tuple val(meta), path(he_image), path(xenium_bundle)
+
+    output:
+    tuple val(meta), path(out_dir), emit: harmonised_output
+    path "versions.yml"           , emit: versions
+
+    script:
+    out_dir = "${meta}_harmonised"
+
+    """
+        harmonise_xenium.py main\\
+            --hematoxylin_eosin_image_uri ${he_image} \\
+            --xenium_bundle_uri ${xenium_bundle} \\
+            --harmonised_dataset_uri ${out_dir} 
+        echo "v1.0.0" > versions.yml
+    """
+
+    stub:
+    out_dir = "${meta}_harmonised"
+
+    """
+    touch ${out_dir}
+    touch versions.yml
+    """
+}

modules/sanger-cellgeni/ml/xeniumharmonise/meta.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "ml_xeniumharmonise"
+
+description: A wrapper module for harmonise_xenium.py script
+keywords:
+  - spatial-transcriptomics(xenium)
+  - ml
+  - he-image
+tools:
+  - "ml":
+      description: ""
+      homepage: ""
+      documentation: ""
+      tool_dev_url: ""
+      doi: ""
+      licence: 
+      identifier: 
+
+## TODO nf-core: Add a description of all of the variables used as input
+input:
+  # Only when we have meta
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+
+    - he_image:
+        type: file
+        description: H&E image file
+
+    - xenium_bundle:
+        type: directory
+        description: output from xenium
+
+
+output:
+  #Only when we have meta
+  - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+
+  - "output_dir":
+        type: directory
+        description: directory for harmonised_xenium outputs.
+
+  - versions:
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+
+authors:
+  - "@dn10-sanger"
+maintainers:
+  - "@dn10-sanger"

modules/sanger-cellgeni/ml/xeniumharmonise/modules.config

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+process {
+    withName: 'ML_XENIUMHARMONISE' {
+        queue          = 'normal'
+        group          = 'cellgeni'
+        cpus           = 1
+        clusterOptions = '-M 8G -R "select[mem>8G] rusage[mem=8G]"'
+        publishDir     = 'results'
+        }
+ }
+

modules/sanger-cellgeni/ml/xeniumharmonise/nf-test.config

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+config {
+    testsDir "."
+    workDir ".nf-test"
+    configFile "tests/nextflow.config"
+
+ }
+