Add FASTQE module (nf-core#6914)

* Add FASTQE module * fix linting * Fix FASTQE * FASTQE: static version in test * Update modules/nf-core/fastqe/meta.yml Co-authored-by: Edmund Miller <[email protected]> --------- Co-authored-by: Edmund Miller <[email protected]>
LouisLeNezet · Oct 31, 2024 · cab0b8f · cab0b8f
1 parent bcf36bc
commit cab0b8f
Show file tree

Hide file tree

Showing 5 changed files with 347 additions and 0 deletions.
diff --git a/modules/nf-core/fastqe/environment.yml b/modules/nf-core/fastqe/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - "bioconda::fastqe=0.3.3"
diff --git a/modules/nf-core/fastqe/main.nf b/modules/nf-core/fastqe/main.nf
@@ -0,0 +1,48 @@
+process FASTQE {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/fastqe:0.3.3--pyhdfd78af_0':
+        'biocontainers/fastqe:0.3.3--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(fastq)
+
+    output:
+    tuple val(meta), path("*.tsv"), emit: tsv
+    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}"
+    def VERSION = '0.3.3'
+    """
+    fastqe \\
+        $args \\
+        $fastq \\
+        --output ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqe: $VERSION
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def VERSION = '0.3.3'
+    """
+    touch ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqe: $VERSION
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/fastqe/meta.yml b/modules/nf-core/fastqe/meta.yml
@@ -0,0 +1,50 @@
+name: "fastqe"
+description: fastqe is a bioinformatics command line tool that uses emojis to represent and analyze genomic data.
+keywords:
+  - quality control
+  - fastq
+  - emoji
+  - visualization
+tools:
+  - fastqe:
+      description: "A tool for visualizing FASTQ file quality using emoji"
+      homepage: "https://github.com/fastqe/fastqe"
+      documentation: "https://github.com/fastqe/fastqe#readme"
+      tool_dev_url: "https://github.com/fastqe/fastqe"
+      doi: "10.21105/joss.02400"
+      licence: ["MIT"]
+      identifier: "biotools:fastqe"
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+    - fastq:
+        type: file
+        description: |
+          List of input FastQ files of size 1 and 2 for single-end and paired-end data,
+          respectively.
+
+output:
+  - tsv:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.tsv":
+          type: file
+          description: Text file containing emoji
+          pattern: "*.tsv"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+
+authors:
+  - "@adamrtalbot"
+maintainers:
+  - "@adamrtalbot"
diff --git a/modules/nf-core/fastqe/tests/main.nf.test b/modules/nf-core/fastqe/tests/main.nf.test
@@ -0,0 +1,100 @@
+// nf-core modules test fastqe
+nextflow_process {
+
+    name "Test Process FASTQE"
+    script "../main.nf"
+    process "FASTQE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "fastqe"
+
+    test("sarscov2 single-end [fastq]") {
+
+        when {
+            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) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [fastq]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [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 single-end [fastq] - stub") {
+
+    options "-stub"
+        when {
+            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) ]
+                ])
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2 paired-end [fastq] - stub") {
+
+    options "-stub"
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [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() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/fastqe/tests/main.nf.test.snap b/modules/nf-core/fastqe/tests/main.nf.test.snap
@@ -0,0 +1,142 @@
+{
+    "sarscov2 single-end [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dbbf45cfa1fab97d81e8de840958233b"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,dbbf45cfa1fab97d81e8de840958233b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-31T10:18:03.83777"
+    },
+    "sarscov2 paired-end [fastq]": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,aceceddba6e4b5a968d54a6db46238da"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dbbf45cfa1fab97d81e8de840958233b"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,aceceddba6e4b5a968d54a6db46238da"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,dbbf45cfa1fab97d81e8de840958233b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-31T10:16:30.591658"
+    },
+    "sarscov2 paired-end [fastq] - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dbbf45cfa1fab97d81e8de840958233b"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,dbbf45cfa1fab97d81e8de840958233b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-31T10:18:09.501789"
+    },
+    "sarscov2 single-end [fastq]": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.tsv:md5,16d66ef19b5f2694aaeae9c3727c3a61"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,dbbf45cfa1fab97d81e8de840958233b"
+                ],
+                "tsv": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.tsv:md5,16d66ef19b5f2694aaeae9c3727c3a61"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,dbbf45cfa1fab97d81e8de840958233b"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-31T10:16:23.822551"
+    }
+}