diff --git a/modules/vardictjava/main.nf b/modules/vardictjava/main.nf new file mode 100644 index 00000000..d52e15dd --- /dev/null +++ b/modules/vardictjava/main.nf @@ -0,0 +1,77 @@ +// 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 VARDICTJAVA { + tag "$meta.id" + label 'process_medium' + + // TODO nf-core: List required Conda package(s). + // Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10"). + // For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems. + // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below. + conda (params.enable_conda ? "bioconda::vardict-java=1.8.3" : null) + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/vardict-java:1.8.3--hdfd78af_0': + 'quay.io/biocontainers/vardict-java:1.8.3--hdfd78af_0' }" + + 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) + path(reference_fasta) + path(regions_of_interest) + + 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 ;) + """ + vardict-java \\ + $args \\ + -b $bam \\ + -th $task.cpus \\ + -n $prefix \\ + -G $reference_fasta \\ + $regions_of_interest \\ + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + vardictjava: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' )) + END_VERSIONS + """ +} diff --git a/modules/vardictjava/meta.yml b/modules/vardictjava/meta.yml new file mode 100644 index 00000000..e8c55de3 --- /dev/null +++ b/modules/vardictjava/meta.yml @@ -0,0 +1,51 @@ +name: "vardictjava" +## TODO nf-core: Add a description of the module and list keywords +description: write your description here +keywords: + - sort +tools: + - "vardictjava": + ## TODO nf-core: Add a description and other details for the software below + description: "Java port of the VarDict variant discovery program" + homepage: "None" + documentation: "None" + tool_dev_url: "None" + doi: "" + licence: "['MIT']" + +## 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: + - "@nvnieuwk" diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml index 4d8ce0b5..8ca9f2e2 100644 --- a/tests/config/pytest_modules.yml +++ b/tests/config/pytest_modules.yml @@ -1908,6 +1908,10 @@ unzip: - modules/unzip/** - tests/modules/unzip/** +vardictjava: + - modules/vardictjava/** + - tests/modules/vardictjava/** + variantbam: - modules/variantbam/** - tests/modules/variantbam/** diff --git a/tests/modules/vardictjava/main.nf b/tests/modules/vardictjava/main.nf new file mode 100644 index 00000000..8a714b2b --- /dev/null +++ b/tests/modules/vardictjava/main.nf @@ -0,0 +1,15 @@ +#!/usr/bin/env nextflow + +nextflow.enable.dsl = 2 + +include { VARDICTJAVA } from '../../../modules/vardictjava/main.nf' + +workflow test_vardictjava { + + input = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_bam'], checkIfExists: true) + ] + + VARDICTJAVA ( input ) +} diff --git a/tests/modules/vardictjava/nextflow.config b/tests/modules/vardictjava/nextflow.config new file mode 100644 index 00000000..5dc176a9 --- /dev/null +++ b/tests/modules/vardictjava/nextflow.config @@ -0,0 +1,8 @@ +process { + + publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } + + withName: VARDICTJAVA { + ext.args = '' + } +} \ No newline at end of file diff --git a/tests/modules/vardictjava/test.yml b/tests/modules/vardictjava/test.yml new file mode 100644 index 00000000..73c647af --- /dev/null +++ b/tests/modules/vardictjava/test.yml @@ -0,0 +1,12 @@ +## TODO nf-core: Please run the following command to build this file: +# nf-core modules create-test-yml vardictjava +- name: "vardictjava" + command: nextflow run ./tests/modules/vardictjava -entry test_vardictjava -c ./tests/config/nextflow.config -c ./tests/modules/vardictjava/nextflow.config + tags: + - "vardictjava" + # + files: + - path: "output/vardictjava/test.bam" + md5sum: e667c7caad0bc4b7ac383fd023c654fc + - path: output/vardictjava/versions.yml + md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b