dysgu_updated

modules/nf-core/dysgu/environment.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+name: "dysgu"
+channels:
+  - conda-forge
+  - bioconda
+  - defaults
+dependencies:
+  - "bioconda::dysgu=1.6.2"

modules/nf-core/dysgu/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 DYSGU {
+    tag "$meta.id"
+    label 'process_medium'
+
+    // TODO nf-core: List required Conda package(s).
+    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
+    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
+    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/dysgu:latest':
+        'biocontainers/dysgu:latest' }"
+
+    input:
+    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
+    //               MUST be provided as an input via a Groovy Map called "meta".
+    //               This information may not be required in some instances e.g. indexing reference genome files:
+    //               https://github.com/nf-core/modules/blob/master/modules/nf-core/bwa/index/main.nf
+    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
+    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
+    tuple val(meta), path(input_bam), path(input_bam_index)
+    tuple val(meta2), path(reference_fasta), path(reference_fasta.fai)
+    tuple val(meta3), path(temp_dir)
+
+    output:
+    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
+    tuple val(meta), path("*.vcf"), emit: vcf
+    // TODO nf-core: List additional required output channels/values here
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
+    //               If the software is unable to output a version number on the command-line then it can be manually specified
+    //               e.g. https://github.com/nf-core/modules/blob/master/modules/nf-core/homer/annotatepeaks/main.nf
+    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
+    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
+    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
+    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
+    // TODO nf-core: Please replace the example samtools command below with your module's command
+    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
+    """
+    dysgu run \\
+        $reference \\
+        $temp_dir \\
+        $input_bam \\
+        > ${prefix}.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        dysgu: \$(dysgu --version 2>&1)
+    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 ${prefix}.vcf
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        dysgu: \$(dysgu --version 2>&1)
+    END_VERSIONS
+    """
+}

modules/nf-core/dysgu/meta.yml

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+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
+name: "dysgu"
+## TODO nf-core: Add a description of the module and list keywords
+description: Dysgu calls structural variants (SVs) from mapped sequencing reads. It is designed for accurate and efficient detection of structural variations.
+keywords:
+  - structural variants
+  - sv
+  - vcf
+tools:
+  - dysgu:
+      description: Structural variant caller for mapped sequencing data
+      homepage: https://github.com/kcleal/dysgu
+      documentation: https://github.com/kcleal/dysgu/blob/master/README.rst
+      tool_dev_url: https://github.com/kcleal/dysgu
+      doi: "10.1093/nar/gkac039"
+      licence: ["GPL-3.0-or-later"]
+version: "1.6.2"
+
+## TODO nf-core: Add a description of all of the variables used as input
+input:
+  # Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'sample1', single_end:false ]`
+
+## TODO nf-core: Delete / customise this example input
+  - input_bam:
+      type: file
+      description: Input BAM file
+      pattern: "*.bam"
+  - input_bam_index:
+      type: file
+      description: BAM index file
+      pattern: "*.bai"
+  - fasta:
+      type: file
+      description: Genome reference FASTA file
+      pattern: "*.{fa,fasta}"
+  - meta3:
+      type: map
+      description: |
+        Groovy Map containing reference information
+        e.g. [ id:'genome' ]
+  - fai:
+      type: file
+      description: Genome reference FASTA index file
+      pattern: "*.{fa.fai,fasta.fai}"
+  - temp_dir:
+      type: directory
+      description: Temporary directory for Dysgu
+
+## TODO nf-core: Add a description of all of the variables used as output
+
+output:
+  #Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. [ id:'test', single_end:false ]
+  - vcf:
+      type: file
+      description: VCF file with identified structural variants
+      pattern: "*.vcf"
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+## TODO nf-core: Delete / customise this example output
+
+authors:
+  - "@kcleal"
+maintainers:
+  - "@kcleal"

modules/nf-core/dysgu/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 dysgu
+nextflow_process {
+
+    name "Test Process DYSGU"
+    script "../main.nf"
+    process "DYSGU"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "dysgu"
+
+    // 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/dysgu/tests/tags.yml

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