Prior cons buildpriors [DRAFT]

modules/nf-core/priorcons/build_priors/environment.yml

@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::priorcons=0.1.0"

modules/nf-core/priorcons/build_priors/main.nf

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+process PRIORCONS_BUILDPRIORS {
+    tag "$meta.id"
+    label 'process_low'
+
+    // TODO pending the container and singularity image being available with priorcons installed.
+    conda "${moduleDir}/environment.yml"
+    // container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    //     'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
+    //     'biocontainers/YOUR-TOOL-HERE' }"
+
+    input:
+    tuple val(meta), path(alignment)  // Input alignment FASTA file
+    val   ref_id                       // Reference sequence ID
+
+    output:
+    tuple val(meta), path("*.parquet"), emit: priors
+    path "versions.yml"               , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    priorcons \\
+        build-priors \\
+        --input ${alignment} \\
+        --ref ${ref_id} \\
+        --output ${prefix}.parquet \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        priorcons: \$(priorcons --version 2>&1 | sed 's/priorcons //')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.parquet
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        priorcons: \$(priorcons --version 2>&1 | sed 's/priorcons //')
+    END_VERSIONS
+    """
+}

modules/nf-core/priorcons/build_priors/meta.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "priorcons_buildpriors"
+description: Build empirical priors from alignment data for consensus sequence
+  generation
+keywords:
+  - alignment
+  - priors
+  - consensus
+  - genomics
+tools:
+  - "priorcons":
+      description: "Tool for integrating consensus sequences using prior information."
+      homepage: "https://github.com/zhliUU/PriorCons"
+      documentation: "https://github.com/zhliUU/PriorCons"
+      tool_dev_url: "https://github.com/zhliUU/PriorCons"
+      licence: ["MIT"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1' ]`
+    - alignment:
+        type: file
+        description: Multiple sequence alignment file
+        pattern: "*.aln"
+        ontologies:
+          - edam: "http://edamontology.org/format_1984" # Plain text alignment format
+  - ref_id:
+      type: string
+      description: Reference sequence ID within the alignment file
+
+output:
+  priors:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1' ]`
+      - "*.parquet":
+          type: file
+          description: Empirical priors data in Parquet format
+          pattern: "*.parquet"
+          ontologies: []
+  versions:
+    - "versions.yml":
+        type: file
+        description: File containing software versions
+        pattern: "versions.yml"
+        ontologies:
+          - edam: "http://edamontology.org/format_3750" # YAML
+
+authors:
+  - "@zhliUU"
+maintainers:
+  - "@zhliUU"

modules/nf-core/priorcons/build_priors/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process PRIORCONS_BUILDPRIORS"
+    script "../main.nf"
+    process "PRIORCONS_BUILDPRIORS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "priorcons"
+    tag "priorcons/buildpriors"
+
+    test("build_priors_testfiles") {
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'rsv_test' ],
+                    file('https://raw.githubusercontent.com/GERMAN00VP/PriorCons/b518f3725b2cc8820222ea52024a0a63f9e6dfe1/rsv_files/build_priors_testfiles/build_priors_test.aln', checkIfExists: true)
+                ]
+                input[1] = 'RSV_BD'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.priors
+                ).match() }
+            )
+        }
+
+    }
+
+    test("build_priors_testfiles - stub") {
+
+        options "-stub"
+
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+            process {
+                """
+                input[0] = [
+                    [ id:'rsv_test' ],
+                    file('https://raw.githubusercontent.com/GERMAN00VP/PriorCons/b518f3725b2cc8820222ea52024a0a63f9e6dfe1/rsv_files/build_priors_testfiles/build_priors_test.aln', checkIfExists: true)
+                ]
+                input[1] = 'RSV_BD'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.versions,
+                    process.out.priors
+                ).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/priorcons/build_priors/tests/main.nf.test.snap

@@ -0,0 +1,42 @@
+{
+    "build_priors_testfiles - stub": {
+        "content": [
+            [
+                "versions.yml:md5,7555426e5737f1dc9bc4f261c31536e2"
+            ],
+            [
+                [
+                    {
+                        "id": "rsv_test"
+                    },
+                    "rsv_test.parquet:md5,d41d8cd98f00b204e9800998ecf8427e"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-29T15:05:15.403088"
+    },
+    "build_priors_testfiles": {
+        "content": [
+            [
+                "versions.yml:md5,7555426e5737f1dc9bc4f261c31536e2"
+            ],
+            [
+                [
+                    {
+                        "id": "rsv_test"
+                    },
+                    "rsv_test.parquet:md5,c10fe51463dd23c5aa34fb39ccac9586"
+                ]
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-29T15:04:13.584116"
+    }
+}