From ab512be9aa86851b6e3ee664e019d7d6dcd0cb81 Mon Sep 17 00:00:00 2001 From: drpatelh Date: Thu, 6 Aug 2020 11:31:52 +0100 Subject: [PATCH] Initial commit --- software/SOFTWARE/TOOL/main.nf | 85 ++++++++++++++++++++++++++++++++++ 1 file changed, 85 insertions(+) create mode 100644 software/SOFTWARE/TOOL/main.nf diff --git a/software/SOFTWARE/TOOL/main.nf b/software/SOFTWARE/TOOL/main.nf new file mode 100644 index 00000000..4363a5f1 --- /dev/null +++ b/software/SOFTWARE/TOOL/main.nf @@ -0,0 +1,85 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +// TODO nf-core: All of these TODO statements can be deleted after the relevant changes have been made. +// 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 "options" is a Groovy Map that MUST be provided in the "input:" section of the process. +// 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. + +// TODO nf-core: Process name MUST be all uppercase, +// "SOFTWARE" and (ideally) "TOOL" MUST be all one word separated by an "_". +process SOFTWARE_TOOL { + // TODO nf-core: If a meta map of sample information is NOT provided in "input:" section + // change tag value to another appropriate input value e.g. tag "$fasta" + tag "$meta.id" + // TODO nf-core: Provide appropriate resource label for process as listed in the nf-core pipeline template below: + // https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/conf/base.config#L29 + label 'process_medium' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + // TODO nf-core: If a meta map of sample information is NOT provided in "input:" section + // change "publish_id:meta.id" to initialise an empty string e.g. "publish_id:''". + saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + + // TODO nf-core: Fetch "docker pull" address for latest Biocontainer image of software: e.g. https://biocontainers.pro/#/tools/samtools + // If required, multi-tool containers may also be available and are usually named to start with "mulled". + container "quay.io/biocontainers/samtools:1.10--h9402c20_2" + + // TODO nf-core: List required Conda packages. + // Software MUST be pinned to channel (i.e. "bioconda") and version (i.e. "1.10") as in the example below. + // Pinning the build too e.g. "bioconda::samtools=1.10=h9402c20_2" is not currently a requirement. + conda (params.conda ? "bioconda::samtools=1.10" : null) + + 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/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. + tuple val(meta), path(reads) + // TODO nf-core: List additional required input channels/values here + val options + + output: + // TODO nf-core: Named file extensions MUST be emitted for ALL output channels + // TODO nf-core: If meta is provided in "input:" section then it MUST be added to ALL output channels (except version) + tuple val(meta), path("*.bam"), emit: bam + // TODO nf-core: List additional required output channels/values here + path "*.version.txt", emit: version + + script: + def software = getSoftwareName(task.process) + def ioptions = initOptions(options) + // TODO nf-core: If a meta map of sample information is NOT provided in "input:" section delete the line below + def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${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/software/homer/annotatepeaks/main.nf + // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$ioptions.args" variable + // 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 indent the command appropriately (4 spaces!!) to help with readability ;) + """ + software tool \\ + $ioptions.args \\ + --threads $task.cpus \\ + $reads \\ + > ${prefix}.bam + + echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt + """ +}