idemux test_data.config (#5391)

* idemux test_data.config

* add idemux module

* idemux test bugfix

* update idemux stub

* fix typos

* test_data.config update

* updated test snapshot

* fix conda version specification

---------

Co-authored-by: vsc41362 vscuser <vsc41362@gligar08.gastly.os>

modules/nf-core/idemux/LICENSE

@@ -0,0 +1,30 @@
+Software License
+Lexogen software on github.com
+
+This license governs use of the Lexogen RNA-Seq kit product accompanying idemux software ("software"). If you use the software, you accept this license. If you do not accept the license, do not use the software.
+
+1. Definitions
+
+The terms "reproduction" ("Vervielfältigung"), "derivative works" ("bearbeitete Werke") and "distribution" ("Verbreitung") have the same meaning here as under mandatory applicable Austrian copyright law.
+
+A "contribution" is the original software, or any additions or changes to the software.
+
+A "contributor" is any person that distributes its contribution under this license.
+
+2.  Grant of License
+
+Subject to the terms of this license, including the license conditions and limitations in section 3, for any non-commercial usage each contributor grants you a non-exclusive, worldwide, royalty-free copyright license to reproduce its contribution, prepare derivative works of its contribution, and distribute its contribution or any derivative works that you create.
+
+Commercial usage shall be allowed exclusively in connection with Lexogen RNA-Seq kit products.
+
+3. Conditions and Limitations
+
+(A) This license does not grant you rights to use any contributors' name, logo, or trademarks.
+
+(B) This license does not grant you rights to use any contributors' patent or patent application.
+
+(C) If you distribute any portion of the software, you must retain all copyright, trademark, and attribution notices that are present in the software.
+
+(D) If you distribute any portion of the software in source code form, you may do so only under this license by including a complete copy of this license with your distribution. If you distribute any portion of the software in compiled or object code form, you may only do so under a license that complies with this license.
+
+(E) The software is licensed "as-is." You bear the risk of using it. The contributors give no express warranties, guarantees or conditions. You may have additional consumer rights under your local laws which this license cannot change. To the extent permitted under your local laws, the contributors exclude the implied warranties of merchantability, fitness for a particular purpose and non-infringement.

modules/nf-core/idemux/environment.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "idemux"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::idemux=0.1.6"

modules/nf-core/idemux/main.nf

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+process IDEMUX {
+    tag "$meta.id"
+    label 'process_high'
+
+    conda "bioconda::idemux=0.1.6"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/idemux:0.1.6--pyhdfd78af_0':
+        'biocontainers/idemux:0.1.6--pyhdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(reads), path(samplesheet)
+
+    output:
+    tuple val(meta), path("[!undetermined]*.fastq.gz")          , emit: fastq
+    tuple val(meta), path("undetermined_R?.fastq.gz")  , optional:true, emit: undetermined
+    path "demultipexing_stats.tsv" , emit: stats
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+
+    """
+    idemux \\
+        --r1 ${reads[0]} \\
+        --r2 ${reads[1]} \\
+        --sample-sheet ${samplesheet} \\
+        --out . \\
+        $args
+
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        idemux: \$(idemux --version |& sed '1!d ; s/idemux //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+
+    """
+    echo -e "sample_name\twritten_reads" > demultipexing_stats.tsv
+
+    sed 1d ${samplesheet} | while IFS=, read -r sampleName _ _ _; do
+        touch "\${sampleName}_R1.fastq"
+        touch "\${sampleName}_R2.fastq"
+        echo -e "\${sampleName}\t100" >> demultipexing_stats.tsv
+    done
+
+    touch undetermined_R1.fastq
+    touch undetermined_R2.fastq
+    gzip *.fastq
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        idemux: \$(idemux --version |& sed '1!d ; s/idemux //')
+    END_VERSIONS
+    """
+}

modules/nf-core/idemux/meta.yml

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+name: idemux
+description: Demultiplex paired-end FASTQ files from QuantSeq-Pool
+keywords:
+  - demultiplex
+  - lexogen
+  - fastq
+tools:
+  - idemux:
+      description: |
+        A Lexogen tool for demultiplexing and index error correcting fastq files. Works with Lexogen i7, i5 and i1 barcodes.
+      homepage: https://github.com/Lexogen-Tools/idemux
+      documentation: https://github.com/Lexogen-Tools/idemux
+      tool_dev_url: https://github.com/Lexogen-Tools/idemux
+      licence: ["LEXOGEN"]
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'NVQ', lane:1 ]
+  - reads:
+      type: file
+      description: |
+        List of input FastQ files
+      pattern: "Undetermined_S*.fastq.gz"
+  - samplesheet:
+      type: file
+      description: Input samplesheet
+      pattern: "*.{csv}"
+output:
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - fastq:
+      type: file
+      description: Demultiplexed sample FASTQ files
+      pattern: "*.fastq.gz"
+  - undetermined:
+      type: file
+      description: Optional undetermined sample FASTQ files
+      pattern: "Undetermined_R?.fastq.gz"
+  - stats:
+      type: file
+      description: Demultiplexing Stats
+      pattern: "demultipexing_stats.tsv"
+authors:
+  - "@jaanckae"
+maintainers:
+  - "@jaanckae"

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

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+nextflow_process {
+
+    name "Test Process IDEMUX"
+    script "../main.nf"
+    process "IDEMUX"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "idemux"
+
+
+    test("idemux - fastq") {
+        when {
+            process {
+                """                
+                input[0] = [
+                    [ id:'NVQ', lane:1 ],
+                    [
+                        file(params.test_data['homo_sapiens']['lexogen']['i7_i5_i1_read_1'], checkIfExists: true),
+                        file(params.test_data['homo_sapiens']['lexogen']['i7_i5_i1_read_2'], checkIfExists: true)
+                    ],
+                    file(params.test_data['homo_sapiens']['lexogen']['i7_i5_i1_sample_sheet'])
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.stats,
+                    process.out.versions,
+                    process.out.fastq,
+                ).match() }
+            )
+        }
+
+    }
+
+    test("idemux - fastq - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """                
+                input[0] = [
+                    [ id:'NVQ', lane:1 ],
+                    [
+                        file(params.test_data['homo_sapiens']['lexogen']['i7_i5_i1_read_1'], checkIfExists: true),
+                        file(params.test_data['homo_sapiens']['lexogen']['i7_i5_i1_read_2'], checkIfExists: true)
+                    ],
+                    file(params.test_data['homo_sapiens']['lexogen']['i7_i5_i1_sample_sheet'])
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.stats,
+                    process.out.versions,
+                    process.out.fastq,
+                ).match() }
+            )
+        }
+
+    }
+
+}