add seqtk_comp

modules/nf-core/seqtk/comp/environment.yml

@@ -0,0 +1,6 @@
+---
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::seqtk=1.4"

modules/nf-core/seqtk/comp/main.nf

@@ -0,0 +1,48 @@
+
+process SEQTK_COMP {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/seqtk:1.4--h577a1d6_3':
+        'biocontainers/seqtk:1.4--h577a1d6_3' }"
+
+    input:
+    tuple val(meta), path(fastx)
+
+    output:
+    tuple val(meta), path("*.seqtk_stats.tsv"), emit: seqtk_stats
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    seqtk comp \\
+        ${args} \\
+        ${fastx} > ${prefix}.seqtk_stats.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqtk: \$(seqtk |& sed '/Version/!d; s/.* //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    echo "" > ${prefix}.seqtk_stats.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        seqtk: \$(seqtk |& sed '/Version/!d; s/.* //')
+    END_VERSIONS
+    """
+}

modules/nf-core/seqtk/comp/meta.yml

@@ -0,0 +1,51 @@
+name: "seqtk_comp"
+description: Computes sequence statistics from FASTQ or FASTA files
+keywords:
+  - seqtk
+  - comp
+  - fastx
+
+tools:
+  - "seqtk_comp":
+      description: |
+        Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. 
+        The seqtk comp command computes base composition, sequence length, and GC content for quality control.
+
+      homepage: https://github.com/lh3/seqtk
+      documentation: https://docs.csc.fi/apps/seqtk/
+      tool_dev_url: https://github.com/lh3/seqtk
+      licence: ["MIT"]
+      identifier: biotools:seqtk
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'sample1' ]
+    - fastx:
+        type: file
+        description: A FASTQ or FASTA file
+        pattern: "*.{fastq,fq,fasta,fa,fas,fna}{,.gz}"
+
+output:
+  - seqtk_stats:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'sample1', single_end:false ]
+      - "*.seqtk_stats.tsv":
+          type: file
+          description: The output TSV file summarizing sequence statistics with columns for sequence name, length, counts of A, C, G, T, and N bases, and GC content percentage."
+          pattern: "*.seqtk_stats.tsv"
+
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@sainsachiko"
+maintainers:
+  - "@sainsachiko"

modules/nf-core/seqtk/comp/tests/main.nf.test

@@ -0,0 +1,60 @@
+nextflow_process {
+
+    name "Test Process SEQTK_COMP"
+    script "../main.nf"
+    process "SEQTK_COMP"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "seqtk"
+    tag "seqtk/comp"
+
+    test("bacteroides_fragilis - fasta") {
+
+        when {
+            process {
+                """                
+                input[0] = [
+                    [ id:'test', single_end:true ],
+                    file( params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+            with(process.out.seqtk_stats[0]) {
+                assert path(get(1)).text.contains("NZ_CP069563.1")
+            }
+        }
+
+    }
+
+    test("bacteroides_fragilis - fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """                
+                input[0] = [
+                    [ id:'test', single_end:true ],
+                    file( params.modules_testdata_base_path + 'genomics/prokaryotes/bacteroides_fragilis/genome/genome.fna.gz', checkIfExists: true),
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
+

modules/nf-core/seqtk/comp/tests/main.nf.test.snap

@@ -0,0 +1,72 @@
+{
+    "bacteroides_fragilis - fasta": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.seqtk_stats.tsv:md5,46c8788954c64c718a799c0f6a41ecdc"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,f374db7a2510fc66d62d68e309971657"
+                ],
+                "seqtk_stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.seqtk_stats.tsv:md5,46c8788954c64c718a799c0f6a41ecdc"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f374db7a2510fc66d62d68e309971657"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2025-03-26T19:53:51.1946864"
+    },
+    "bacteroides_fragilis - fasta - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.seqtk_stats.tsv:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,f374db7a2510fc66d62d68e309971657"
+                ],
+                "seqtk_stats": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.seqtk_stats.tsv:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,f374db7a2510fc66d62d68e309971657"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2025-03-26T19:53:56.444250615"
+    }
+}

modules/nf-core/seqtk/comp/tests/tags.yml

@@ -0,0 +1,2 @@
+seqtk/mergepe:
+  - "modules/nf-core/seqtk/comp/**"