|
0
|
1 process NANOPLOT {
|
|
|
2 tag "$meta.id"
|
|
|
3 label 'process_micro'
|
|
|
4
|
|
|
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}NanoPlot${params.fs}1.43.0" : null)
|
|
|
6 conda (params.enable_conda ? "conda-forge::plotly bioconda::nanoplot=1.43.0" : null)
|
|
|
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
|
8 'https://depot.galaxyproject.org/singularity/nanoplot:1.42.0--pyhdfd78af_0' :
|
|
|
9 'quay.io/biocontainers/nanoplot:1.42.0--pyhdfd78af_0' }"
|
|
|
10
|
|
|
11 input:
|
|
|
12 tuple val(meta), path(ontfile)
|
|
|
13
|
|
|
14 output:
|
|
|
15 tuple val(meta), path("*.html"), emit: html
|
|
|
16 tuple val(meta), path("*.png") , emit: png, optional: true
|
|
|
17 tuple val(meta), path("*.txt") , emit: txt
|
|
|
18 tuple val(meta), path("*.log") , emit: log
|
|
|
19 path "versions.yml" , emit: versions
|
|
|
20
|
|
|
21 when:
|
|
|
22 task.ext.when == null || task.ext.when
|
|
|
23
|
|
|
24 script:
|
|
|
25 def args = task.ext.args ?: ''
|
|
|
26 def input_file = ("$ontfile".endsWith(".fastq.gz") || "$ontfile".endsWith(".fq.gz")) ? "--fastq ${ontfile}" :
|
|
|
27 ("$ontfile".endsWith(".txt")) ? "--summary ${ontfile}" : ''
|
|
|
28 """
|
|
|
29 NanoPlot \\
|
|
|
30 $args \\
|
|
|
31 -t $task.cpus \\
|
|
|
32 $input_file
|
|
|
33
|
|
|
34 cat <<-END_VERSIONS > versions.yml
|
|
|
35 "${task.process}":
|
|
|
36 nanoplot: \$(echo \$(NanoPlot --version 2>&1) | sed 's/^.*NanoPlot //; s/ .*\$//')
|
|
|
37 END_VERSIONS
|
|
|
38 """
|
|
|
39 } |
