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cleanup TODO's

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Matthias De Smet 2022-04-27 11:18:58 +02:00 committed by GitHub
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modules/vardictjava/main.nf
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@ -1,48 +1,19 @@
// 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:
@ -51,15 +22,7 @@ process VARDICTJAVA {
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 \\