From 8a948266a8cfdd42e9c6257a06d26fe221dadd54 Mon Sep 17 00:00:00 2001
From: DarkoCucin <137320136+DarkoCucin@users.noreply.github.com>
Date: Thu, 31 Oct 2024 15:25:36 +0100
Subject: [PATCH] Adding sequali module to nf-core modules (#6896)

* Adding sequali module

* Update modules/nf-core/sequali/environment.yml

typo fixed

Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com>

* Getting a snapsot for JSON file (without meta field)

* modifying main.nf.test

* Adding naming check for JSON file

---------

Co-authored-by: Eirini (Irene) Liampa <irini.liampa@gmail.com>
Co-authored-by: Louis LE NEZET <58640615+LouisLeNezet@users.noreply.github.com>
---
 modules/nf-core/sequali/environment.yml       |   7 +
 modules/nf-core/sequali/main.nf               |  58 +++++
 modules/nf-core/sequali/meta.yml              |  60 +++++
 modules/nf-core/sequali/tests/main.nf.test    | 171 ++++++++++++
 .../nf-core/sequali/tests/main.nf.test.snap   | 245 ++++++++++++++++++
 5 files changed, 541 insertions(+)
 create mode 100644 modules/nf-core/sequali/environment.yml
 create mode 100644 modules/nf-core/sequali/main.nf
 create mode 100644 modules/nf-core/sequali/meta.yml
 create mode 100644 modules/nf-core/sequali/tests/main.nf.test
 create mode 100644 modules/nf-core/sequali/tests/main.nf.test.snap

diff --git a/modules/nf-core/sequali/environment.yml b/modules/nf-core/sequali/environment.yml
new file mode 100644
index 00000000000..b712a24fdd5
--- /dev/null
+++ b/modules/nf-core/sequali/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::sequali=0.12.0
diff --git a/modules/nf-core/sequali/main.nf b/modules/nf-core/sequali/main.nf
new file mode 100644
index 00000000000..718c07171c9
--- /dev/null
+++ b/modules/nf-core/sequali/main.nf
@@ -0,0 +1,58 @@
+process SEQUALI {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'oras://community.wave.seqera.io/library/sequali:0.12.0--c288fa2befb47d0f':
+        'community.wave.seqera.io/library/sequali:0.12.0--07485bec824d914a' }"
+
+    input:
+
+    tuple val(meta), path(reads)
+
+    output:
+
+    tuple val(meta), path("*.html"), emit: html
+    tuple val(meta), path("*.json"), emit: json
+    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 read_1_bam = reads.size() == 1 ? reads : reads[0]
+    def read_2 = reads.size() == 2 ? reads[1]: ""
+
+    """
+    sequali \\
+        $args \\
+        -t $task.cpus \\
+        --html ${prefix}.html \\
+        --json ${prefix}.json \\
+        $read_1_bam \\
+        $read_2
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sequali: \$(sequali --version |& sed '1!d ; s/sequali //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}.html
+    touch ${prefix}.json
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        sequali: \$(sequali --version |& sed '1!d ; s/sequali //')
+    END_VERSIONS
+    """
+}
+
diff --git a/modules/nf-core/sequali/meta.yml b/modules/nf-core/sequali/meta.yml
new file mode 100644
index 00000000000..62dc6e85e00
--- /dev/null
+++ b/modules/nf-core/sequali/meta.yml
@@ -0,0 +1,60 @@
+---
+name: sequali
+description: Sequence quality metrics for FASTQ and uBAM files.
+keywords:
+  - quality_control
+  - qc
+  - preprocessing
+tools:
+  - sequali:
+      description: Fast sequencing quality metrics
+      homepage: "https://github.com/rhpvorderman/sequali"
+      documentation: "https://sequali.readthedocs.io/en/latest/"
+      tool_dev_url: "https://github.com/rhpvorderman/sequali"
+      doi: "10.5281/zenodo.10854010"
+      licence: ["AGPL v3-or-later"]
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'sample1', single_end:false ]`
+
+    - reads:
+        type: file
+        description: Input FASTQ(s) or uBAM file. The format is autodetected and compressed formats are supported.
+        pattern: "*.{fastq,fq,fastq.gz,fq.gz,bam}"
+output:
+  - json:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.json":
+          type: file
+          description: JSON output file.
+          pattern: "*.{json}"
+  - html:
+      - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'sample1', single_end:false ]`
+      - "*.html":
+          type: file
+          description: HTML output file.
+          pattern: "*.{html}"
+
+  - versions:
+      - "versions.yml":
+          type: file
+          description: File containing software versions.
+          pattern: "versions.yml"
+authors:
+  - "@irliampa"
+  - "@DarkoCucin"
+maintainers:
+  - "@irliampa"
+  - "@DarkoCucin"
diff --git a/modules/nf-core/sequali/tests/main.nf.test b/modules/nf-core/sequali/tests/main.nf.test
new file mode 100644
index 00000000000..9876153caf6
--- /dev/null
+++ b/modules/nf-core/sequali/tests/main.nf.test
@@ -0,0 +1,171 @@
+nextflow_process {
+
+    name "Test Process SEQUALI"
+    script "../main.nf"
+    process "SEQUALI"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "sequali"
+
+    test("sarscov2 - fastq single-end [sequali]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ 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 snapshot(
+                    path(process.out.html[0][1]).getFileName().toString(),
+                    path(process.out.json[0][1]).getFileName().toString(),
+                    path(process.out.json[0][1]).json.remove('summary'),
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+        test("sarscov2 - fastq paired-end [sequali]") {
+
+        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(
+                    path(process.out.html[0][1]).getFileName().toString(),
+                    path(process.out.json[0][1]).getFileName().toString(),
+                    path(process.out.json[0][1]).json.remove('summary'),
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+        test("sarscov2 - unaligned bam [sequali]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: true], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.unaligned.bam', checkIfExists: true)])
+                """
+            }
+        }
+
+        then {
+            def json_file = path(process.out.json[0][1]).json.get('summary')
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    path(process.out.html[0][1]).getFileName().toString(),
+                    path(process.out.json[0][1]).getFileName().toString(),
+                    path(process.out.json[0][1]).json.remove('summary'),
+                    process.out.versions
+                ).match() }
+            )
+        }
+
+    }
+
+        test("sarscov2 - fastq single-end - stub[sequali]") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [ 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(
+                    path(process.out.html[0][1]).getFileName().toString(),
+                    path(process.out.json[0][1]).getFileName().toString(),
+                    process.out
+                ).match() }
+            )
+        }
+
+    }
+        test("sarscov2 - fastq paired-end - stub[sequali]") {
+
+        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(
+                    path(process.out.html[0][1]).getFileName().toString(),
+                    path(process.out.json[0][1]).getFileName().toString(),
+                    process.out
+                ).match() }
+            )
+        }
+
+    }
+
+        test("sarscov2 - unaligned bam - stub[sequali]") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of([
+                    [id: 'test', single_end: true], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.unaligned.bam', checkIfExists: true)])
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    path(process.out.html[0][1]).getFileName().toString(),
+                    path(process.out.json[0][1]).getFileName().toString(),
+                    process.out
+                ).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-core/sequali/tests/main.nf.test.snap b/modules/nf-core/sequali/tests/main.nf.test.snap
new file mode 100644
index 00000000000..441c352bea4
--- /dev/null
+++ b/modules/nf-core/sequali/tests/main.nf.test.snap
@@ -0,0 +1,245 @@
+{
+    "sarscov2 - unaligned bam - stub[sequali]": {
+        "content": [
+            "test.html",
+            "test.json",
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,afd9522ef20d5fe27e0b6aab541c7c30"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "json": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,afd9522ef20d5fe27e0b6aab541c7c30"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-31T14:30:30.653577"
+    },
+    "sarscov2 - fastq paired-end [sequali]": {
+        "content": [
+            "test.html",
+            "test.json",
+            {
+                "mean_length": 138.97,
+                "minimum_length": 72,
+                "maximum_length": 151,
+                "total_reads": 100,
+                "q20_reads": 91,
+                "total_bases": 13897,
+                "q20_bases": 12922,
+                "total_gc_bases": 5430,
+                "total_n_bases": 0,
+                "read_pair_info": "Read 1"
+            },
+            [
+                "versions.yml:md5,afd9522ef20d5fe27e0b6aab541c7c30"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-31T14:29:34.748364"
+    },
+    "sarscov2 - fastq single-end - stub[sequali]": {
+        "content": [
+            "test.html",
+            "test.json",
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,afd9522ef20d5fe27e0b6aab541c7c30"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "json": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": true
+                        },
+                        "test.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,afd9522ef20d5fe27e0b6aab541c7c30"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-31T14:30:06.387152"
+    },
+    "sarscov2 - fastq single-end [sequali]": {
+        "content": [
+            "test.html",
+            "test.json",
+            {
+                "mean_length": 138.97,
+                "minimum_length": 72,
+                "maximum_length": 151,
+                "total_reads": 100,
+                "q20_reads": 91,
+                "total_bases": 13897,
+                "q20_bases": 12922,
+                "total_gc_bases": 5430,
+                "total_n_bases": 0,
+                "read_pair_info": null
+            },
+            [
+                "versions.yml:md5,afd9522ef20d5fe27e0b6aab541c7c30"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-31T14:28:42.093895"
+    },
+    "sarscov2 - unaligned bam [sequali]": {
+        "content": [
+            "test.html",
+            "test.json",
+            {
+                "mean_length": 138.97,
+                "minimum_length": 72,
+                "maximum_length": 151,
+                "total_reads": 100,
+                "q20_reads": 91,
+                "total_bases": 13897,
+                "q20_bases": 12922,
+                "total_gc_bases": 5430,
+                "total_n_bases": 0,
+                "read_pair_info": null
+            },
+            [
+                "versions.yml:md5,afd9522ef20d5fe27e0b6aab541c7c30"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-31T14:29:54.657233"
+    },
+    "sarscov2 - fastq paired-end - stub[sequali]": {
+        "content": [
+            "test.html",
+            "test.json",
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,afd9522ef20d5fe27e0b6aab541c7c30"
+                ],
+                "html": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.html:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "json": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test.json:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,afd9522ef20d5fe27e0b6aab541c7c30"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.1",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-10-31T14:30:18.654267"
+    }
+}
\ No newline at end of file