fastqe

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"

modules/nf-core/fastqe/main.nf

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+process FASTQE {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/fastqe:0.3.3--pyhdfd78af_0':
+        'biocontainers/fastqe:0.3.3--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(reads)
+
+    output:
+    tuple val(meta), path("*.txt"), emit: report
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    fastqe \\
+        $reads \\
+        $args \\
+        --output ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqe: \$(fastqe --version 2>&1 | sed 's/fastqe, version //')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastqe: \$(fastqe --version 2>&1 | sed 's/fastqe, version //')
+    END_VERSIONS
+    """
+}

modules/nf-core/fastqe/meta.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "fastqe"
+description: Compute quality stats for FASTQ files and print those stats as emoji
+keywords:
+  - fastq
+  - quality
+  - emoji
+  - qc
+tools:
+  - "fastqe":
+      description: "A tool that converts FASTQ quality scores to emoji for visualization"
+      homepage: "https://github.com/fastqe/fastqe"
+      documentation: "https://github.com/fastqe/fastqe"
+      licence: ['BSD-3-clause']
+
+input:
+  - meta:
+      type: [ "map" ]
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - reads:
+      type: [ "file" ]
+      description: FASTQ file(s)
+      pattern: "*.{fastq,fq,fastq.gz,fq.gz}"
+
+output:
+  - meta:
+      type: [ "map" ]
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - report:
+      type: [ "file" ]
+      description: Text file containing emoji representation of quality scores
+      pattern: "*.txt"
+  - versions:
+      type: [ "file" ]
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@edmundmiller"
+maintainers:
+  - "@edmundmiller"

modules/nf-core/fastqe/tests/main.nf.test

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+nextflow_process {
+
+    name "Test Process FASTQE"
+    script "../main.nf"
+    process "FASTQE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "fastqe"
+
+    test("fastq - single_end") {
+        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() },
+                { assert path(process.out.report[0][1]).readLines().size() > 0 }
+            )
+        }
+    }
+
+    test("fastq - paired_end") {
+        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() },
+                { assert path(process.out.report[0][1]).readLines().size() > 0 }
+            )
+        }
+    }
+
+    test("fastq - single_end - 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() }
+            )
+        }
+    }
+
+}