Add seqkit split2

software/seqkit/split2/functions.nf

@@ -0,0 +1,59 @@
+/*
+ * -----------------------------------------------------
+ *  Utility functions used in nf-core DSL2 module files
+ * -----------------------------------------------------
+ */
+
+/*
+ * Extract name of software tool from process name using $task.process
+ */
+def getSoftwareName(task_process) {
+    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
+}
+
+/*
+ * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
+ */
+def initOptions(Map args) {
+    def Map options = [:]
+    options.args          = args.args ?: ''
+    options.args2         = args.args2 ?: ''
+    options.publish_by_id = args.publish_by_id ?: false
+    options.publish_dir   = args.publish_dir ?: ''
+    options.publish_files = args.publish_files
+    options.suffix        = args.suffix ?: ''
+    return options
+}
+
+/*
+ * Tidy up and join elements of a list to return a path string
+ */
+def getPathFromList(path_list) {
+    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
+    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes
+    return paths.join('/')
+}
+
+/*
+ * Function to save/publish module results
+ */
+def saveFiles(Map args) {
+    if (!args.filename.endsWith('.version.txt')) {
+        def ioptions = initOptions(args.options)
+        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
+        if (ioptions.publish_by_id) {
+            path_list.add(args.publish_id)
+        }
+        if (ioptions.publish_files instanceof Map) {
+            for (ext in ioptions.publish_files) {
+                if (args.filename.endsWith(ext.key)) {
+                    def ext_list = path_list.collect()
+                    ext_list.add(ext.value)
+                    return "${getPathFromList(ext_list)}/$args.filename"
+                }
+            }
+        } else if (ioptions.publish_files == null) {
+            return "${getPathFromList(path_list)}/$args.filename"
+        }
+    }
+}

software/seqkit/split2/main.nf

@@ -0,0 +1,85 @@
+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+// 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/software
+//               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: The key words "MUST", "MUST NOT", "SHOULD", etc. are to be interpreted as described in RFC 2119 (https://tools.ietf.org/html/rfc2119).
+// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
+//               All other parameters MUST be provided as a string i.e. "options.args"
+//               where "params.options" is a Groovy Map that MUST be provided via the addParams section of the including workflow.
+//               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. bwa mem | samtools view -B -T ref.fasta to output BAM instead of SAM.
+// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, "fake files" MAY be used to work around this issue.
+
+params.options = [:]
+def options    = initOptions(params.options)
+
+process SEQKIT_SPLIT2 {
+    tag "$meta.id"
+    label 'process_medium'
+
+    publishDir "${params.outdir}",
+        mode: params.publish_dir_mode,
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
+
+    conda (params.enable_conda ? "bioconda::seqkit=0.15.0" : null)
+
+    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
+        container "https://depot.galaxyproject.org/singularity/seqkit:0.15.0--0"
+    } else {
+        container "quay.io/biocontainers/seqkit:0.15.0--0"
+    }
+
+    input:
+    tuple val(meta), path(read1), path(read2)
+
+    // 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/software/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.
+
+    output:
+    tuple val(meta), path("*.fq.gz"), emit: reads
+    path("*.version.txt")          , emit: version
+
+
+    script:
+    def software = getSoftwareName(task.process)
+
+    //TODO not sure if this is useful here, as the splits need to be named individually, and this would make the prefix the same and the outputname I am afraid.
+    def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
+
+    if(meta.single_end){ //TODO: I guess since optionally inputs are not possible right now, we need two modules, one for single_end and one for paired_end
+    """
+    seqkit \
+        split2 \
+        $options.args \
+        --threads $task.cpus \
+        -1 $read1 \
+        -O $prefix
+
+
+    echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt
+    """
+    } else {
+    """
+    seqkit \
+        split2 \
+        $options.args \
+        --threads $task.cpus \
+        -1 $read1 \
+        -2 $read2 \
+        -O $prefix
+
+    echo \$(seqkit --version 2>&1) | sed 's/^.*seqkit //; s/Using.*\$//' > ${software}.version.txt
+    """
+    }
+}

software/seqkit/split2/meta.yml

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+name: seqkit_split2
+## TODO nf-core: Add a description and keywords
+description: Split single or paired-end fastq.gz files
+keywords:
+    - split
+    - fastq
+tools:
+    - seqkit:
+        ## TODO nf-core: Add a description and other details for the software below
+        description: |
+            Cross-platform and ultrafast toolkit for FASTA/Q file manipulation, written by Wei Shen.
+        homepage: https://github.com/shenwei356/seqkit
+        documentation: https://bioinf.shenwei.me/seqkit/
+        doi: 10.1371/journal.pone.0163962
+## TODO nf-core: If you are using any additional "params" in the main.nf script of the module add them below
+params:
+    - outdir:
+        type: string
+        description: |
+            The pipeline's output directory. By default, the module will
+            output files into `$params.outdir/<SOFTWARE>`
+    - publish_dir_mode:
+        type: string
+        description: |
+            Value for the Nextflow `publishDir` mode parameter.
+            Available: symlink, rellink, link, copy, copyNoFollow, move.
+    - enable_conda:
+        type: boolean
+        description: |
+            Run the module with Conda using the software specified
+            via the `conda` directive
+    - singularity_pull_docker_container:
+        type: boolean
+        description: |
+            Instead of directly downloading Singularity images for use with Singularity,
+            force the workflow to pull and convert Docker containers instead.
+## TODO nf-core: Add a description of all of the variables used as input
+input:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - read1:
+        type: file
+        description: First FastQ file
+        pattern: "*.{fq.gz/fastq.gz}"
+    - read2:
+        type: file
+        description: Second FastQ file
+        pattern: "*.{fq.gz/fastq.gz}"
+## TODO nf-core: Add a description of all of the variables used as output
+output:
+    - meta:
+        type: map
+        description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+    - reads:
+        type: file
+        description: Split fastq files
+        pattern: "*.{fq.gz}"
+    - version:
+        type: file
+        description: File containing software version
+        pattern: "*.{version.txt}"
+authors:
+    - "@FriederikeHanssen"