initiate tbpore modules

main.nf

@@ -96,7 +96,7 @@ workflow {
         NFCORE_TBANALYZER.out.multiqc_report
     )
 }
-
+// Everything seemed okay
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     THE END

modules/tbpore/modules/local/tbpore_cluster/main.nf

@@ -0,0 +1,47 @@
+process TBPORE_CLUSTER {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/tbpore:0.7.1--pyhdfd78af_0':
+        'biocontainers/tbpore:0.7.1--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(consensus_fa)
+
+    output:
+
+    tuple val(meta), path("*.txt"), emit: txt
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    """
+    tbpore cluster $args \\
+        --threads $task.cpus \\
+        $consensus_fa
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tbpore: \$(tbpore --version |& sed s/tbpore, version //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tbpore: \$(tbpore --version |& sed s/tbpore, version //')
+    END_VERSIONS
+    """
+}

modules/tbpore/modules/local/tbpore_cluster/tests/main.nf.test

@@ -0,0 +1,55 @@
+nextflow_process {
+
+    name "Test Process TBPORE_CLUSTER"
+    script "../main.nf"
+    process "TBPORE_CLUSTER"
+
+    setup {
+        run("TBPORE_PROCESS") {
+            script "../../tbpore_process/main.nf"
+
+            params {
+                modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+            }
+
+            process {
+                """
+
+                input[0] = Channel.of([
+                [ id:'test', single_end:true ],
+                    file(
+                        params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz',
+                        checkIfExists: true
+                    )
+                ])
+
+                input[1] = Channel.of(
+                file("/.tbpore/decontamination_db/remove_contam.map-ont.mmi")
+                )
+                """
+            }
+        }
+    }
+
+    test("sarscov2 single end [fastq]") {
+
+        when {
+            params {
+                // define parameters here. Example:
+                outdir = "tests/results"
+            }
+            process {
+                """
+                // input[0] = TBPORE_PROCESS.out.fa | collect
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+}

modules/tbpore/modules/local/tbpore_process/main.nf

@@ -0,0 +1,61 @@
+
+process TBPORE_PROCESS {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/tbpore:0.7.1--pyhdfd78af_0':
+        'biocontainers/tbpore:0.7.1--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fastq)
+    path db
+
+    output:
+    tuple val(meta), path("*.json"), emit: json
+    tuple val(meta), path("*.fa")  , emit: fa
+    tuple val(meta), path("*.bcf") , emit: bcf
+    tuple val(meta), path("*.txt") , emit: txt
+    path "versions.yml"            , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    tbpore process $args \\
+        --threads $task.cpus \\
+        --name $prefix \\
+        --db $db \\
+        $fastq
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tbpore: \$(tbpore --version |& sed s/tbpore, version //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
+    //               Have a look at the following examples:
+    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
+    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
+    """
+    touch ${prefix}.json
+    touch ${prefix}.fa
+    touch ${prefix}.bcf
+    touch ${prefix}.txt
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        tbpore:  \$(tbpore --version |& sed s/tbpore, version //')
+    END_VERSIONS
+    """
+}

modules/tbpore/modules/local/tbpore_process/tests/main.nf.test

@@ -0,0 +1,43 @@
+nextflow_process {
+
+    name "Test Process TBPORE_PROCESS"
+    script "../main.nf"
+    process "TBPORE_PROCESS"
+
+    tag TBPORE_PROCESS
+
+    test("sarscov2 single end fastq") {
+
+        when {
+            params {
+                //define parameters here. Example:
+                modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
+                outdir = "tests/results"
+            }
+            process {
+                """
+                input[0] = Channel.of([
+                    [ id:'test', single_end:true ],
+                    file(
+                        params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz',
+                        checkIfExists: true
+                    )
+                ])
+                input[1] = Channel.fromPath(
+                file("/.tbpore/decontamination_db/remove_contam.map-ont.mmi")
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/tbpore/modules/local/tbpore_process/tests/main.nf.test.snap

@@ -0,0 +1,43 @@
+{
+    "real data fastq": {
+        "content": [
+            {
+                "0": [
+
+                ],
+                "1": [
+
+                ],
+                "2": [
+
+                ],
+                "3": [
+
+                ],
+                "4": [
+
+                ],
+                "bcf": [
+
+                ],
+                "fa": [
+
+                ],
+                "json": [
+
+                ],
+                "txt": [
+
+                ],
+                "versions": [
+
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-03T12:51:08.385030023"
+    }
+}

nf-test.config

@@ -0,0 +1,8 @@
+config {
+
+    testsDir "tests"
+    workDir ".nf-test"
+    configFile "tests/nextflow.config"
+    profile ""
+
+}

tests/nextflow.config

@@ -0,0 +1,5 @@
+/*
+========================================================================================
+    Nextflow config file for running tests
+========================================================================================
+*/