mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-14 05:43:08 +00:00
f3ffa69b8d
* feat(dragmap): Add initial hastable module * feat(dragmap): Add initial align module * test(dragmap): Remove md5sum Forgot sam files have a header. Might pipe this through samtools. * build(dragmap): Add mulled container * chore(dragmap): Update prefix * feat(dragmap): Output a bam file * feat(dragmap): Add log files * Update modules/dragmap/align/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
33 lines
905 B
Text
33 lines
905 B
Text
process DRAGMAP_HASHTABLE {
|
|
tag "$fasta"
|
|
label 'process_high'
|
|
|
|
conda (params.enable_conda ? "bioconda::dragmap=1.2.1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/dragmap:1.2.1--hd4ca14e_0':
|
|
'quay.io/biocontainers/dragmap:1.2.1--hd4ca14e_0' }"
|
|
|
|
input:
|
|
path fasta
|
|
|
|
output:
|
|
path "dragmap" , emit: hashmap
|
|
path "versions.yml" , emit: versions
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
"""
|
|
mkdir dragmap
|
|
dragen-os \\
|
|
--build-hash-table true \\
|
|
--ht-reference $fasta \\
|
|
--output-directory dragmap \\
|
|
$args \\
|
|
--ht-num-threads $task.cpus
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
dragmap: \$(echo \$(dragen-os --version 2>&1))
|
|
END_VERSIONS
|
|
"""
|
|
}
|