Add wittyer as module

modules/nf-core/wittyer/environment.yml

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

modules/nf-core/wittyer/main.nf

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+// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
+//               https://github.com/nf-core/modules/tree/master/modules/nf-core/
+//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
+//               https://nf-co.re/join
+// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
+//               All other parameters MUST be provided using the "task.ext" directive, see here:
+//               https://www.nextflow.io/docs/latest/process.html#ext
+//               where "task.ext" is a string.
+//               Any parameters that need to be evaluated in the context of a particular sample
+//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
+// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
+//               unless there is a run-time, storage advantage in implementing in this way
+//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
+//                 bwa mem | samtools view -B -T ref.fasta
+// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
+//               list (`[]`) instead of a file can be used to work around this issue.
+
+process WITTYER {
+    tag "$meta.id"
+    label 'process_single'
+
+    // TODO nf-core: List required Conda package(s).
+    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
+    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
+    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
+    // conda "${moduleDir}/environment.yml"
+    container "nf-core/wittier:0.3.3"
+    // "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+    //    'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE':
+    //    'biocontainers/YOUR-TOOL-HERE' }"
+
+    input:
+    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
+    //               MUST be provided as an input via a Groovy Map called "meta".
+    //               This information may not be required in some instances e.g. indexing reference genome files:
+    //               https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf
+    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
+    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
+    tuple val(meta), path(query_vcf), path(query_vcf_tbi), path(truth_vcf), path(truth_vcf_tbi), path(bed)
+
+    output:
+    tuple val(meta),    path("*.Stats.json")         , emit: report
+    tuple val(meta),    path("*eval.vcf.gz")         , emit: bench_vcf
+    tuple val(meta),    path("*eval.vcf.gz.tbi")     , emit: bench_vcf_tbi
+    path  "versions.yml" 
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    // Exit if running this module with -profile conda / -profile mamba
+    if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
+        error "WHITTYER module does not support Conda. Please use Docker / Singularity / Podman instead."
+    }
+    def args  = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def regions = bed ? "--includeBed=$bed" : ""
+    """
+    mkdir bench
+    wittyer \\
+        --truthVcf=${truth_vcf} \\
+        --inputVcf=${query_vcf} \\
+        --outputDirectory=bench \\
+        ${regions} \\
+        ${args}
+
+    mv bench/Wittyer.Stats.json ${prefix}.Stats.json
+    mv bench/*.vcf.gz ${prefix}.eval.vcf.gz
+    mv bench/*.vcf.gz.tbi ${prefix}.eval.vcf.gz.tbi
+
+    rm -rf bench
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        wittyer: \$(wittyer --version  |& sed '1!d ; s/witty.er //')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    // TODO nf-core: A stub section should mimic the execution of the original module as best as possible
+    //               Have a look at the following examples:
+    //               Simple example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bcftools/annotate/main.nf#L47-L63
+    //               Complex example: https://github.com/nf-core/modules/blob/818474a292b4860ae8ff88e149fbcda68814114d/modules/nf-core/bedtools/split/main.nf#L38-L54
+    """
+    touch ${prefix}.bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        wittyer: \$(wittyer --version  |& sed '1!d ; s/witty.er //')
+    END_VERSIONS
+    """
+}

modules/nf-core/wittyer/meta.yml

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+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "wittyer"
+description: A large variant benchmarking tool analogous to hap.py for small variants.
+keywords:
+  - structural-variants
+  - benchmarking
+  - vcf
+tools:
+  - "wittyer":
+      description: "Illumina tool for large variant benchmarking"
+      homepage: "https://github.com/Illumina/witty.er"
+      documentation: "https://github.com/Illumina/witty.er"
+      tool_dev_url: "https://github.com/Illumina/witty.er"
+      licence: "['BSD-2']"
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - query_vcf:
+      type: file
+      description: A VCF with called variants to benchmark against the standard
+      pattern: "*.{vcf,vcf.gz}"
+  - query_vcf_index:
+      type: file
+      description: The index of the called VCF (optional)
+      pattern: "*.tbi"
+  - truth_vcf:
+      type: file
+      description: A standard VCF to compare against
+      pattern: "*.{vcf,vcf.gz}"
+  - truth_vcf_index:
+      type: file
+      description: The index of the standard VCF (optional)
+      pattern: "*.tbi"
+  - bed:
+      type: file
+      description: A BED file specifying regions to be included in the analysis (optional)
+      pattern: "*.bed"
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  - report:
+      type: file
+      description: Detailed per-sample-pair, per-svtype, per-bin stats
+      pattern: "*.Stats.json"
+  - bench_vcf:
+      type: file
+      description: Updated query and truth entries merged into one file
+      pattern: "*eval.vcf.gz"
+  - bench_vcf_tbi:
+      type: file
+      description: Index of merged query and truth entries VCF file
+      pattern: "*eval.vcf.gz.tbi"
+authors:
+  - "@famosab"
+maintainers:
+  - "@famosab"

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

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+// TODO nf-core: Once you have added the required tests, please run the following command to build this file:
+// nf-core modules test wittyer
+nextflow_process {
+
+    name "Test Process WITTYER"
+    script "../main.nf"
+    process "WITTYER"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "wittyer"
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used
+    test("sarscov2 - bam") {
+
+        // TODO nf-core: If you are created a test for a chained module
+        // (the module requires running more than one process to generate the required output)
+        // add the 'setup' method here.
+        // You can find more information about how to use a 'setup' method in the docs (https://nf-co.re/docs/contributing/modules#steps-for-creating-nf-test-for-chained-modules).
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+                // See https://nf-co.re/docs/contributing/tutorials/nf-test_assertions for more information and examples.
+            )
+        }
+
+    }
+
+    // TODO nf-core: Change the test name preferably indicating the test-data and file-format used but keep the " - stub" suffix.
+    test("sarscov2 - bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                // TODO nf-core: define inputs of the process here. Example:
+
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+                    ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+                //TODO nf-core: Add all required assertions to verify the test output.
+            )
+        }
+
+    }
+
+}

modules/nf-core/wittyer/tests/tags.yml

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+wittyer:
+  - "modules/nf-core/wittyer/**"