mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
c5235a983d
* Add blacklist of modules that shouldn't be updated to .nf-core.yml * nf-core modules bump-versions for all modules * Remove TODO statements identified by linting * Fix md5sums for failing tests * Fix more tests
44 lines
1.4 KiB
Text
44 lines
1.4 KiB
Text
// Import generic module functions
|
|
include { initOptions; saveFiles; getSoftwareName } from './functions'
|
|
|
|
params.options = [:]
|
|
options = initOptions(params.options)
|
|
|
|
process IQTREE {
|
|
tag "$alignment"
|
|
label 'process_medium'
|
|
publishDir "${params.outdir}",
|
|
mode: params.publish_dir_mode,
|
|
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:[]) }
|
|
|
|
conda (params.enable_conda ? 'bioconda::iqtree=2.1.4_beta' : null)
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
|
container "https://depot.galaxyproject.org/singularity/iqtree:2.1.4_beta--hdcc8f71_0"
|
|
} else {
|
|
container "quay.io/biocontainers/iqtree:2.1.4_beta--hdcc8f71_0"
|
|
}
|
|
|
|
input:
|
|
path alignment
|
|
val constant_sites
|
|
|
|
output:
|
|
path "*.treefile", emit: phylogeny
|
|
path "*.version.txt", emit: version
|
|
|
|
script:
|
|
def software = getSoftwareName(task.process)
|
|
def fconst_args = constant_sites ? "-fconst $constant_sites" : ''
|
|
def memory = task.memory.toString().replaceAll(' ', '')
|
|
"""
|
|
iqtree \\
|
|
$fconst_args \\
|
|
$options.args \\
|
|
-s $alignment \\
|
|
-nt AUTO \\
|
|
-ntmax $task.cpus \\
|
|
-mem $memory \\
|
|
|
|
echo \$(iqtree -version 2>&1) | sed 's/^IQ-TREE multicore version \\([0-9\\.]*\\) .*\$/\\1/' > ${software}.version.txt
|
|
"""
|
|
}
|