Started adding kneaddata_readcount module

modules/local/kneaddata/readcounts/main.nf

@@ -0,0 +1,48 @@
+process KNEADDATA_KNEADDATA {
+    tag "${meta.id}"
+    label 'process_high'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/kneaddata:0.12.0--pyhdfd78af_1':
+        'biocontainers/kneaddata:0.12.0--pyhdfd78af_1' }"
+
+    input:
+    tuple val(meta), path(fastq_gz)
+    path (kneaddata_db)
+
+    output:
+    tuple val(meta), path("${prefix}_kneaddata_paired_{1,2}.fastq.gz")  , emit: preprocessed_reads
+    tuple val(meta), path("${prefix}_kneaddata.log")                    , emit: kneaddata_log
+    path "versions.yml"                                                 , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    kneaddata_read_count_table \\
+        --input ./ \\
+        --output ${prefix}_kneaddata_read_count.tsv \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        kneaddata: \$(echo \$(kneaddata --version 2>&1 | sed 's/^.*v//' ))
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    ${prefix}_kneaddata_read_count.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        kneaddata: \$(echo \$(kneaddata --version 2>&1 | sed 's/^.*v//' ))
+    END_VERSIONS
+    """
+}

subworkflows/local/fastq_read_preprocessing_kneaddata/tests/main.nf.test

@@ -0,0 +1,41 @@
+nextflow_workflow {
+
+    name "Test Subworkflow: FASTQ_READ_PREPROCESSING_KNEADDATA"
+    script "../main.nf"
+    workflow "FASTQ_READ_PREPROCESSING_KNEADDATA"
+
+    tag "subworkflows"
+    tag "subworkflows_local"
+    tag "fastq_read_preprocessing_kneaddata"
+    tag "fastq_read_preprocessing_kneaddata_default"
+
+
+    test("Parameters: default") {
+
+        when {
+            params {
+                outdir              = "$outputDir"
+            }
+            workflow {
+                """
+                input[0] = Channel.of(
+                    [
+                        [ id: 'test' ],
+                        [
+                            file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                            file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+                        ]
+                    ]
+                )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}