add module for yak (#6053)

* add yak count * add nf.test * added snap * added snap * removed tailing spaces * added keywords in meta * change file type * Update modules/nf-core/yak/count/tests/main.nf.test Co-authored-by: Joon Klaps <[email protected]> * Update modules/nf-core/yak/count/main.nf Co-authored-by: Joon Klaps <[email protected]> * Update modules/nf-core/yak/count/main.nf Co-authored-by: Joon Klaps <[email protected]> * add pe test in nf test * fixed format * test * Update modules/nf-core/yak/count/meta.yml Co-authored-by: Joon Klaps <[email protected]> * Update modules/nf-core/yak/count/main.nf Co-authored-by: Joon Klaps <[email protected]> * Update modules/nf-core/yak/count/meta.yml Co-authored-by: Joon Klaps <[email protected]> * Update modules/nf-core/yak/count/tests/main.nf.test Co-authored-by: Joon Klaps <[email protected]> * Update modules/nf-core/yak/count/meta.yml Co-authored-by: Joon Klaps <[email protected]> * Update modules/nf-core/yak/count/main.nf Co-authored-by: Joon Klaps <[email protected]> * Update modules/nf-core/yak/count/main.nf Co-authored-by: Joon Klaps <[email protected]> * minor changes in meta, regenerated snap * minor changes in meta, regenerated snap * removed pe test * removed spaces * fixed format * removed tests and modify nf test order --------- Co-authored-by: Joon Klaps <[email protected]>
nf-core · Jul 31, 2024 · e5ac715 · e5ac715
1 parent 4133cae
commit e5ac715
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diff --git a/modules/nf-core/yak/count/environment.yml b/modules/nf-core/yak/count/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "yak_count"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::yak=0.1"
diff --git a/modules/nf-core/yak/count/main.nf b/modules/nf-core/yak/count/main.nf
@@ -0,0 +1,49 @@
+process YAK_COUNT {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/yak:0.1--he4a0461_4':
+        'biocontainers/yak:0.1--he4a0461_4' }"
+
+    input:
+    tuple val(meta), path(fastq)
+
+    output:
+    tuple val(meta), path("*.yak"), emit: yak
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    input_command = meta.single_end ? "${fastq}" : "<(zcat ${fastq}) <(zcat ${fastq})"
+    """
+    yak \\
+        count \\
+        $args \\
+        -t${task.cpus} \\
+        -o ${prefix}.yak \\
+        $input_command
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        yak: \$(yak version)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.yak
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        yak: \$(yak version)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/yak/count/meta.yml b/modules/nf-core/yak/count/meta.yml
@@ -0,0 +1,47 @@
+name: "yak_count"
+description: a tool to build k-mer hash table for fasta and fastq files
+keywords:
+  - kmer
+  - fastq
+  - sequence
+  - count
+  - assembly
+
+tools:
+  - "yak":
+      description: "Yet another k-mer analyzer"
+      homepage: "https://github.com/lh3/yak"
+      documentation: "https://github.com/lh3/yak/blob/master/README.md"
+      tool_dev_url: "https://github.com/lh3/yak"
+      licence: ["MIT"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - fastq:
+      type: file
+      description: reads fastq/fasta file
+      pattern: "*.{fastq.gz,fq.gz,fasta.gz,fa.gz}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - yak:
+      type: file
+      description: k-mer hash table of input
+      pattern: "*.{yak}"
+
+authors:
+  - "@yumisims"
+maintainers:
+  - "@yumisims"
diff --git a/modules/nf-core/yak/count/tests/main.nf.test b/modules/nf-core/yak/count/tests/main.nf.test
@@ -0,0 +1,81 @@
+nextflow_process {
+
+    name "Test Process YAK_COUNT"
+    script "../main.nf"
+    process "YAK_COUNT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "yak"
+    tag "yak/count"
+
+    test("sarscov2 - Illumina - se") {
+
+        when {
+            process {
+                """                
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - Illumina - pe") {
+
+        when {
+            process {
+                """                
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    [ file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true),
+                     file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true)]
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - Illumina - se - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                 """                
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.modules_testdata_base_path + "genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/yak/count/tests/main.nf.test.snap b/modules/nf-core/yak/count/tests/main.nf.test.snap
@@ -0,0 +1,107 @@
+{
+    "sarscov2 - Illumina - se": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.yak:md5,0f7375059550949b7ba619a984ece2da"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,bf1f473f0df39c185adfaf52c9701874"
+                ],
+                "versions": [
+                    "versions.yml:md5,bf1f473f0df39c185adfaf52c9701874"
+                ],
+                "yak": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.yak:md5,0f7375059550949b7ba619a984ece2da"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-30T13:14:15.064795726"
+    },
+    "sarscov2 - Illumina - se - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.yak:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,bf1f473f0df39c185adfaf52c9701874"
+                ],
+                "versions": [
+                    "versions.yml:md5,bf1f473f0df39c185adfaf52c9701874"
+                ],
+                "yak": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.yak:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-30T13:14:36.315145428"
+    },
+    "sarscov2 - Illumina - pe": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.yak:md5,f4d1b22744d1ba9619bf7b66c89ecf10"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,bf1f473f0df39c185adfaf52c9701874"
+                ],
+                "versions": [
+                    "versions.yml:md5,bf1f473f0df39c185adfaf52c9701874"
+                ],
+                "yak": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.yak:md5,f4d1b22744d1ba9619bf7b66c89ecf10"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-07-30T13:14:25.971171004"
+    }
+}
diff --git a/modules/nf-core/yak/count/tests/tags.yml b/modules/nf-core/yak/count/tests/tags.yml
@@ -0,0 +1,2 @@
+yak/count:
+  - "modules/nf-core/yak/count/**"