Added new module for Toulligqc

modules/nf-core/toulligqc/environment.yml

@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "toulligqc"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::toulligqc=2.5.4"

modules/nf-core/toulligqc/main.nf

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+process TOULLIGQC {
+    label 'process_low'
+    tag "$meta.id"
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/toulligqc:2.5.4--pyhdfd78af_0':
+        'biocontainers/toulligqc:2.5.4--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(seq_summary)
+    tuple val(meta), path(fastq)
+    tuple val(meta), path(bam)
+
+    output:
+    tuple val(meta), path("*/*.data")   , emit: report_data
+    path "*/*.html"                     , emit: report_html, optional: true
+    path "*/images/*.html"              , emit: plots_html
+    path "*/images/plotly.min.js"       , emit: plotly_js
+
+    path "versions.yml" , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def seq_summary_input = seq_summary ? "--sequencing-summary-source ${seq_summary}" : ""
+    def fastq_input = fastq ? "--fastq ${fastq}" : ""
+    def bam_input = bam ? "--bam ${bam}" : ""
+
+    """
+    toulligqc ${seq_summary_input} \\
+                ${fastq_input} \\
+                ${bam_input} \\
+                $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        toulligqc: \$(toulligqc --version 2>&1)
+    END_VERSIONS
+    """
+}

modules/nf-core/toulligqc/meta.yml

@@ -0,0 +1,66 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "toulligqc"
+description: "A post sequencing QC tool for Oxford Nanopore sequencers"
+keywords:
+  - nanopore sequencing
+  - quality control
+  - genomics
+tools:
+  - "toulligqc":
+      description: "A post sequencing QC tool for Oxford Nanopore sequencers"
+      homepage: https://github.com/GenomiqueENS/toulligQC
+      documentation: https://github.com/GenomiqueENS/toulligQC
+      tool_dev_url: https://github.com/GenomiqueENS/toulligQC
+      licence: ["CECILL-2.1"]
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - seq_summary:
+      type: file
+      description: Basecaller sequencing summary source
+      pattern: "*.txt"
+  - fastq:
+      type: file
+      description: FASTQ file (necessary if no sequencing summary file)
+      pattern: "*.{fq,fastq,fq.gz,fastq.gz}"
+  - bam:
+      type: file
+      description: BAM file (necessary if no sequencing summary file)
+      pattern: "*.bam"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - report_data:
+      type: file
+      description: Report data emitted from toulligqc
+      pattern: "*.data"
+  - report_html:
+      type: file
+      description: Report data in html format
+      pattern: "*.html"
+  - plots_html:
+      type: file
+      description: Plots emitted in html format
+      pattern: "*.html"
+  - plotly_js:
+      type: file
+      description: Plots emitted from toulligqc
+      pattern: "plotly.min.js"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@Salome-Brunon"
+maintainers:
+  - "@Salome-Brunon"

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

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+nextflow_process {
+
+    name "Test Process TOULLIGQC"
+    script "../main.nf"
+    process "TOULLIGQC"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "toulligqc"
+
+    test("sarscov2 - nanopore sequencing_summary") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['sarscov2']['nanopore']['test2_sequencing_summary'], checkIfExists: true)
+                    ]
+                input[1] = [
+                    [],
+                    []
+                    ]
+                input[2] = [
+                    [],
+                    []
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.report_data.get(0).get(1)).readLines()[11..74]).match() },
+                { assert process.out.report_html[0] ==~ ".*/report.html"}
+            )
+        }
+
+    }
+
+    test("sarscov2 - nanopore fastq") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [],
+                    []
+                    ]
+                input[1] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true)
+                    ]
+                input[2] = [
+                    [],
+                    []
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.report_data.get(0).get(1)).readLines()[11..67]).match() },
+                { assert process.out.report_html[0] ==~ ".*/report.html"}
+            )
+        }
+
+    }
+
+    test("sarscov2 - nanopore bam") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [],
+                    []
+                    ]
+                input[1] = [
+                    [],
+                    []
+                    ]
+                input[2] = [
+                    [ id:'test' ], // meta map
+                    file(params.test_data['sarscov2']['nanopore']['test_sorted_bam'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.report_data.get(0).get(1)).readLines()[11..74]).match() },
+                { assert process.out.report_html[0] ==~ ".*/report.html"}
+            )
+        }
+
+    }
+}