Baysor module

modules/nf-core/baysor/preview/main.nf

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+process BAYSOR_PREVIEW {
+    tag '$meta.id'
+    label 'process_high_memory'
+    container "docker.io/segonzal/baysor:0.7.1"
+
+    input:
+    tuple val(meta), path(transcripts_csv)
+    path(config_toml)
+
+    output:
+    tuple val(meta), path("preview.html"), emit: preview_html
+    path("preview_preview_log.log"),       emit: preview_log
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "BAYSOR_PREVIEW module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def args = task.ext.args ?: ''
+    def prefix  = task.ext.prefix ?: "${meta.id}"
+    def VERSION = "0.7.1"
+
+    """
+    baysor preview ${transcripts_csv} -c ${config_toml} $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        baysor: $VERSION
+    END_VERSIONS
+    """
+
+    stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "BAYSOR_PREVIEW module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def args = task.ext.args ?: ''
+    def prefix  = task.ext.prefix ?: "${meta.id}"
+    def VERSION = "0.7.1"
+
+    """
+    touch preview.html
+    touch preview_preview_log.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        baysor: $VERSION
+    END_VERSIONS
+    """
+}

modules/nf-core/baysor/preview/meta.yml

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+name: "baysor_preview"
+description: Preview run for visualization of data.
+keywords:
+  - exploratory-data-analysis
+tools:
+  - "baysor":
+    description: "Baysor is a tool that segments cells using spatial gene expression maps. Optionally, segmentation masks can be given as additional input."
+    homepage: "https://kharchenkolab.github.io/Baysor/dev/"
+    documentation: "https://kharchenkolab.github.io/Baysor/dev/"
+    tool_dev_url: "https://github.com/kharchenkolab/Baysor"
+    doi: "https://doi.org/10.1038/s41587-021-01044-w"
+    licence: ["MIT license"]
+    identifier:
+
+## baysor_preview requires a transcript map of the data and a configuration file with argument values
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - transcripts_csv:
+        type: file
+        description: CSV file
+        pattern: "*.csv"
+
+  - config_toml:
+    type: file
+    description: TOML file with config arguments
+    pattern: "*.toml"
+
+## segmentation results
+output:
+  - preview_html:
+      - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+      - "preview.html":
+        type: file
+        description: segmentation preview
+        pattern: "preview.html"
+
+  - preview_log:
+    type: file
+    description: |
+      Log file with summary statistics of preview
+    pattern: "preview_preview_log.log"
+
+
+authors:
+  - "@sebgoti8"
+maintainers:
+  - "@sebgoti8"

modules/nf-core/baysor/preview/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process BAYSOR_PREVIEW"
+    script "../main.nf"
+    process "BAYSOR_PREVIEW"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "baysor"
+
+    test("baysor preview - html") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'spatial_omics/xenium/homo_sapiens/spatial_gene_expression.csv', checkIfExists: true),
+                ]
+
+                input[1] = [
+                    file(params.modules_testdata_base_path + 'generic/config/config_baysor.toml', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+            )
+        }
+
+    }
+
+    test("baysor preview - html - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'spatial_omics/xenium/homo_sapiens/spatial_gene_expression.csv', checkIfExists: true),
+                ]
+
+                input[1] = [
+                    file(params.modules_testdata_base_path + 'generic/config/config_baysor.toml' , checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+            )
+        }
+
+    }
+
+}

modules/nf-core/baysor/preview/tests/tags.yml

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+baysor:
+  - "modules/nf-core/baysor/preview/**"

modules/nf-core/baysor/run/main.nf

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+process BAYSOR_RUN {
+    tag '$meta.id'
+    label 'process_high_memory'
+    container "docker.io/segonzal/baysor:0.7.1"
+
+    input:
+    tuple val(meta), path(transcripts_csv)
+    path(config_toml)
+
+    output:
+    tuple val(meta), path("*segmentation.csv"), emit: segmentation
+    path("*.json"),           emit: polygons
+    path("*.toml"),           emit: params
+    path("*.log"),            emit: log
+    path("*.loom"),           emit: loom
+    path("segmentation_cell_stats.csv"), emit: stats
+    path "versions.yml"                      , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "BAYSOR_RUN module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def args = task.ext.args ?: ''
+    def prefix  = task.ext.prefix ?: "${meta.id}"
+    def VERSION = "0.7.1"
+
+    """
+    baysor run ${transcripts_csv} -c ${config_toml} $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        baysor: $VERSION
+    END_VERSIONS
+    """
+
+    stub:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "BAYSOR_RUN module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def args = task.ext.args ?: ''
+    def prefix  = task.ext.prefix ?: "${meta.id}"
+    def VERSION = "0.7.1"
+
+    """
+    touch segmentation.csv
+    touch segmentation_polygons_2d.json
+    touch segmentation_log.log
+    touch segmentation_counts.loom
+    touch segmentation_cell_stats.csv
+    touch segmentation_params.dump.toml
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        baysor: $VERSION
+    END_VERSIONS
+    """
+}