Add priorcons module [DRAFT]

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

@@ -0,0 +1,73 @@
+
+process PRIORCONS_INTEGRATE_CONSENSUS {
+    tag "$meta.id"
+    label 'process_low'
+
+    // Activate conda env
+    conda "${moduleDir}/environment.yml"
+
+    //container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    //'https://depot.galaxyproject.org/singularity/priorcons:0.1.0--pyhdfd78af_0' :
+    //'quay.io/biocontainers/priorcons:0.1.0--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(input_aln), val(ref_id), path(prior_parquet)
+
+    output:
+    tuple val(meta), path("${meta.id}_output"), emit: results
+    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 integrate-consensus \\
+        --input $input_aln \\
+        --ref $ref_id \\
+        --prior $prior_parquet \\
+        --output_dir ${prefix}_output \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        priorcons: \$(priorcons --version 2>&1 | head -n1 || echo "v0.1.0")
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    mkdir -p ${prefix}_output
+
+    # Create stub out files
+    echo ">${prefix}_integrated_consensus" > ${prefix}_output/${prefix}-INTEGRATED.fasta
+    echo "ATCGATCGATCG" >> ${prefix}_output/${prefix}-INTEGRATED.fasta
+
+    # Create windows_trace.csv stub
+    cat <<-EOF > ${prefix}_output/windows_trace.csv
+    window_start,window_end,score,selected_sequence
+    1,100,0.95,mapping_consensus
+    101,200,0.87,abacas_consensus
+    EOF
+
+    # Create qc.json stub
+    cat <<-EOF > ${prefix}_output/qc.json
+    {
+        "total_windows": 150,
+        "mapping_selected": 95,
+        "abacas_selected": 55,
+        "average_score": 0.91
+    }
+    EOF
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        priorcons: "v0.1.0"
+    END_VERSIONS
+    """
+}

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

@@ -0,0 +1,55 @@
+name: PRIORCONS_INTEGRATE_CONSENSUS
+description: Integrate consensus sequences using the PriorCons tool with prior
+  probabilities for improved consensus calling
+keywords:
+  - consensus
+  - integration
+  - priorcons
+  - sequencing
+  - viral
+  - genomics
+authors:
+  - "@GERMAN00VP"
+
+tools:
+  - priorcons:
+      description: "Tool for integrating consensus sequences using prior probabilities"
+      homepage: "https://github.com/GERMAN00VP/PriorCons"
+      documentation: "https://github.com/GERMAN00VP/PriorCons"
+      doi: "no DOI available"
+      licence: ["APL-1.0"]
+      identifier: ""
+
+input:
+  - - meta:
+        type: map
+        description: "Groovy Map containing sample information, e.g. [ id:'sample1',
+          single_end:false ]"
+    - input_aln:
+        type: file
+        description: "Input alignment file containing reference, mapping consensus,
+          and ABACAS consensus sequences (exactly in that order)"
+        pattern: "*.{aln,fasta,fa}"
+        ontologies: []
+    - ref_id:
+        type: string
+        description: "Reference identifier for the consensus sequence"
+    - prior_parquet:
+        type: file
+        description: "Prior probabilities table in Parquet format"
+        pattern: "*.parquet"
+
+        ontologies: []
+output:
+  results:
+    - - meta:
+          type: map
+          description: "Groovy Map containing sample information"
+      - ${meta.id}_output:
+          type: directory
+          description: "Output directory containing integrated consensus and QC files"
+  versions:
+    - versions.yml:
+        type: file
+        description: "File containing software versions"
+        ontologies: []

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

@@ -0,0 +1,60 @@
+// nf-core modules test priorcons
+nextflow_process {
+
+    name "Test Process PRIORCONS_INTEGRATE_CONSENSUS"
+    script "../main.nf"
+    process "PRIORCONS_INTEGRATE_CONSENSUS"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "priorcons"
+    tag "priorcons/integrate_consensus"
+
+    test("rsv - alignment and priors") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_sample' ],
+                    file("https://raw.githubusercontent.com/GERMAN00VP/PriorCons/refs/heads/main/rsv_files/test_aln.aln", checkIfExists: true),
+                    "RSV_BD",
+                    file("https://raw.githubusercontent.com/GERMAN00VP/PriorCons/refs/heads/main/rsv_files/RSV_priors/RSVBD_win100_ovlp50_priors.parquet", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("rsv - alignment and priors - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test_sample' ],
+                    file("https://raw.githubusercontent.com/GERMAN00VP/PriorCons/refs/heads/main/rsv_files/test_aln.aln", checkIfExists: true),
+                    "RSV_BD",
+                    file("https://raw.githubusercontent.com/GERMAN00VP/PriorCons/refs/heads/main/rsv_files/RSV_priors/RSVBD_win100_ovlp50_priors.parquet", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assertAll(
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

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

@@ -0,0 +1,84 @@
+{
+    "rsv - alignment and priors - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_sample"
+                        },
+                        [
+                            "qc.json:md5,71a1cb3e5374a26598ac9007827dd93d",
+                            "test_sample-INTEGRATED.fasta:md5,36171c110b33501cc6e914c833701a5b",
+                            "windows_trace.csv:md5,f30c5600c891536a8267fd842ccc6bb7"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,a071d22d6ee41cb1c1f6ef405449cf88"
+                ],
+                "results": [
+                    [
+                        {
+                            "id": "test_sample"
+                        },
+                        [
+                            "qc.json:md5,71a1cb3e5374a26598ac9007827dd93d",
+                            "test_sample-INTEGRATED.fasta:md5,36171c110b33501cc6e914c833701a5b",
+                            "windows_trace.csv:md5,f30c5600c891536a8267fd842ccc6bb7"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,a071d22d6ee41cb1c1f6ef405449cf88"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-29T14:34:35.32780199"
+    },
+    "rsv - alignment and priors": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test_sample"
+                        },
+                        [
+                            "qc.json:md5,4b4e02ba2ea95927346978c8e70c64bb",
+                            "test_aln-INTEGRATED.fasta:md5,bf934389f1e443d6d629c40388a54ebc",
+                            "windows_trace.csv:md5,313ba6650eededbe120b6efb9e31daa6"
+                        ]
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,00491161097c256612e9ba72d13a183f"
+                ],
+                "results": [
+                    [
+                        {
+                            "id": "test_sample"
+                        },
+                        [
+                            "qc.json:md5,4b4e02ba2ea95927346978c8e70c64bb",
+                            "test_aln-INTEGRATED.fasta:md5,bf934389f1e443d6d629c40388a54ebc",
+                            "windows_trace.csv:md5,313ba6650eededbe120b6efb9e31daa6"
+                        ]
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,00491161097c256612e9ba72d13a183f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-29T14:31:17.242646235"
+    }
+}