Skeleton

modules/gatk/realignertargetcreator/main.nf

@@ -0,0 +1,75 @@
+// 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
+//               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 GATK_REALIGNERTARGETCREATOR {
+    tag "$meta.id"
+    label 'process_low'
+
+    // TODO nf-core: List required Conda package(s).
+    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
+    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
+    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
+    conda (params.enable_conda ? "bioconda::gatk=3.8" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gatk:3.8--hdfd78af_11':
+        'quay.io/biocontainers/gatk:3.8--hdfd78af_11' }"
+
+    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/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(bam)
+
+    output:
+    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
+    tuple val(meta), path("*.bam"), emit: bam
+    // 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/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 ;)
+    """
+    samtools \\
+        sort \\
+        $args \\
+        -@ $task.cpus \\
+        -o ${prefix}.bam \\
+        -T $prefix \\
+        $bam
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
+}

modules/gatk/realignertargetcreator/meta.yml

@@ -0,0 +1,51 @@
+name: "gatk_realignertargetcreator"
+## TODO nf-core: Add a description of the module and list keywords
+description: write your description here
+keywords:
+  - sort
+tools:
+  - "gatk":
+      ## TODO nf-core: Add a description and other details for the software below
+      description: "The full Genome Analysis Toolkit (GATK) framework, license restricted."
+      homepage: "None"
+      documentation: "None"
+      tool_dev_url: "None"
+      doi: ""
+      licence: "['https://software.broadinstitute.org/gatk/download/licensing', 'https://www.broadinstitute.org/gatk/about/#licensing', 'BSD']"
+
+## 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:'test', single_end:false ]
+  # 
+  ## TODO nf-core: Delete / customise this example input
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+## 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 ]
+  # 
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+  ## TODO nf-core: Delete / customise this example output
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+authors:
+  - "@jfy133"

tests/config/pytest_modules.yml

@@ -715,6 +715,10 @@ gamma/gamma:
   - modules/gamma/gamma/**
   - tests/modules/gamma/gamma/**
 
+gatk/realignertargetcreator:
+  - modules/gatk/realignertargetcreator/**
+  - tests/modules/gatk/realignertargetcreator/**
+
 gatk4/applybqsr:
   - modules/gatk4/applybqsr/**
   - tests/modules/gatk4/applybqsr/**

tests/modules/gatk/realignertargetcreator/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK_REALIGNERTARGETCREATOR } from '../../../../modules/gatk/realignertargetcreator/main.nf'
+
+workflow test_gatk_realignertargetcreator {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    GATK_REALIGNERTARGETCREATOR ( input )
+}

tests/modules/gatk/realignertargetcreator/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}

tests/modules/gatk/realignertargetcreator/test.yml

@@ -0,0 +1,14 @@
+## TODO nf-core: Please run the following command to build this file:
+#                nf-core modules create-test-yml gatk/realignertargetcreator
+- name: "gatk realignertargetcreator"
+  command: nextflow run ./tests/modules/gatk/realignertargetcreator -entry test_gatk_realignertargetcreator -c ./tests/config/nextflow.config -c ./tests/modules/gatk/realignertargetcreator/nextflow.config
+  tags:
+    - "gatk"
+    #
+    - "gatk/realignertargetcreator"
+    #
+  files:
+    - path: "output/gatk/test.bam"
+      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: output/gatk/versions.yml
+      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b