Added new module for Toulligqc (nf-core#5131)

* ADD: working toulligqc as module * ToulligQC module passed tests * [automated] Fix linting with Prettier * Remove whitespaces * Update main.nf * Update main.nf * Update modules/nf-core/toulligqc/meta.yml Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/nf-core/toulligqc/meta.yml Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/nf-core/toulligqc/meta.yml Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * Update modules/nf-core/toulligqc/main.nf Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * UPDATE: added fastq as input option * Update environment.yml * UPDATE: moved to ToulligQC v2.5.4 and added BAM as input file option * Update modules/nf-core/toulligqc/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * Update modules/nf-core/toulligqc/meta.yml Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * UPDATE: added meta map to module * UPDATE: added stub section to module * Update modules/nf-core/toulligqc/main.nf Co-authored-by: James A. Fellows Yates <jfy133@gmail.com> * FIX: pass seq_summarry, fastq, bam as one tuple --------- Co-authored-by: nf-core-bot <core@nf-co.re> Co-authored-by: Jonathan Manning <jonathan.manning@seqera.io> Co-authored-by: Friederike Hanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>
RSC-RP · Mar 28, 2024 · 49423bb · 49423bb
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diff --git a/modules/nf-core/toulligqc/environment.yml b/modules/nf-core/toulligqc/environment.yml
@@ -0,0 +1,9 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "toulligqc"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::toulligqc=2.5.4"
diff --git a/modules/nf-core/toulligqc/main.nf b/modules/nf-core/toulligqc/main.nf
@@ -0,0 +1,64 @@
+process TOULLIGQC {
+    label 'process_low'
+    tag "$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), path(fastq), 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} \\
+        --output-directory ${prefix} \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        toulligqc: \$(toulligqc --version 2>&1)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir ${prefix}
+    mkdir ${prefix}/images
+    touch ${prefix}/report.data
+    touch ${prefix}/images/Correlation_between_read_length_and_PHRED_score.html
+    touch ${prefix}/images/Distribution_of_read_lengths.html
+    touch ${prefix}/images/PHRED_score_density_distribution.html
+    touch ${prefix}/images/Read_count_histogram.html
+    touch ${prefix}/images/plotly.min.js
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        toulligqc: \$(toulligqc --version 2>&1)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/toulligqc/meta.yml b/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"
diff --git a/modules/nf-core/toulligqc/tests/main.nf.test b/modules/nf-core/toulligqc/tests/main.nf.test
@@ -0,0 +1,105 @@
+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),
+                    [],
+                    []
+                    ]
+                """
+            }
+        }
+
+        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] = [
+                    [ id:'test' ], // meta map
+                    [],
+                    file(params.test_data['sarscov2']['nanopore']['test_fastq_gz'], checkIfExists: true),
+                    []
+                    ]
+                """
+            }
+        }
+
+        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] = [
+                    [ 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"}
+            )
+        }
+
+    }
+    test("sarscov2 - naopore bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+                    [],
+                    [],
+                    file(params.test_data['sarscov2']['nanopore']['test_sorted_bam'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success }
+            )
+        }
+    }
+}