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Subazini TK 2022-05-13 15:40:50 +02:00 committed by Edmund Miller
parent 2a15bc2ac0
commit 8b4c5742c9
1 changed files with 1 additions and 22 deletions
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23
modules/hmtnote/main.nf
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@ -2,28 +2,15 @@ process HMTNOTE {
tag "$meta.id"
label 'process_low'
// TODO nf-core: List required Conda package(s).
// Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
// For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
// TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
conda (params.enable_conda ? "bioconda::hmtnote=0.7.2" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/hmtnote:0.7.2--pyhdfd78af_0':
'quay.io/biocontainers/hmtnote:0.7.2--pyhdfd78af_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(vcf)
output:
// TODO nf-core: Named file extensions MUST be emitted for ALL output channels
tuple val(meta), path("*_annotated.vcf"), emit: vcf
// TODO nf-core: List additional required output channels/values here
path "versions.yml" , emit: versions
when:
@ -32,15 +19,7 @@ process HMTNOTE {
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 ;)
"""
hmtnote \\
annotate \\