mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 06:03:10 +00:00
a0443e2c54
* Update main.nf * Update meta.yml * Re-add logos as not staged in a way that works with MultiQC config files * Update main.nf * Remove now unnecessary input channel * Remove unused channel from tests * Update hAMRonization to 1.1.1 and add hAMRonization farGene * Fix hamronizatio ntests * Prettier * Fix fargene linting * Correct file * Fix fargene output * Apply suggestions from code review Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com> * Fix summarise tests * Prettier * Fix incorrect quotes in tags Co-authored-by: Jasmin F <73216762+jasmezz@users.noreply.github.com>
40 lines
1.2 KiB
Text
40 lines
1.2 KiB
Text
process HMMCOPY_GENERATEMAP {
|
|
tag "$bam"
|
|
label 'process_long'
|
|
|
|
// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
|
|
conda (params.enable_conda ? "bioconda::hmmcopy=0.1.1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/hmmcopy:0.1.1--h2e03b76_7':
|
|
'quay.io/biocontainers/hmmcopy:0.1.1--h2e03b76_7' }"
|
|
|
|
input:
|
|
path fasta
|
|
|
|
output:
|
|
path "*.map.bw" , emit: bigwig
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def VERSION = '0.1.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
|
|
"""
|
|
# build required indexes
|
|
generateMap.pl -b \\
|
|
$args \\
|
|
$fasta
|
|
|
|
# run
|
|
generateMap.pl \\
|
|
$args \\
|
|
$fasta
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
hmmcopy: \$(echo $VERSION)
|
|
END_VERSIONS
|
|
"""
|
|
}
|