mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
f2264c1052
* added scramble/clusteridentifier * linting * added cluster_analysis * added a comment to the mei ref * added reference comments * linting
53 lines
2.1 KiB
Text
53 lines
2.1 KiB
Text
process SCRAMBLE_CLUSTERANALYSIS {
|
|
tag "$meta.id"
|
|
label 'process_single'
|
|
|
|
conda (params.enable_conda ? "bioconda::scramble=1.0.1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/scramble:1.0.1--h779adbc_1':
|
|
'quay.io/biocontainers/scramble:1.0.1--h779adbc_1' }"
|
|
|
|
input:
|
|
tuple val(meta), path(clusters)
|
|
path fasta
|
|
path mei_ref
|
|
|
|
output:
|
|
tuple val(meta), path("*_MEIs.txt") , optional:true, emit: meis_tab
|
|
tuple val(meta), path("*_PredictedDeletions.txt") , optional:true, emit: dels_tab
|
|
tuple val(meta), path("*.vcf") , optional:true, emit: vcf
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
|
def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
|
|
|
|
def blastdb = args.contains("--eval-dels") ? "makeblastdb -in ${fasta} -parse_seqids -title ${fasta} -dbtype nucl -out ${fasta}" : ""
|
|
def reference = fasta ? "--ref `pwd`/${fasta}" : ""
|
|
|
|
// The default file for the MEI reference is a file that's inside the container
|
|
def mei_reference = mei_ref ? "`pwd`/${mei_ref}" : "/usr/local/share/scramble/resources/MEI_consensus_seqs.fa"
|
|
|
|
def blastdb_version = args.contains("--eval-dels") ? "makeblastdb: \$(echo \$(makeblastdb -version 2>&1) | head -n 1 | sed 's/^makeblastdb: //; s/+ Package.*\$//')" : ""
|
|
"""
|
|
${blastdb}
|
|
|
|
Rscript --vanilla /usr/local/share/scramble/bin/SCRAMble.R \\
|
|
--install-dir /usr/local/share/scramble/bin \\
|
|
${args} \\
|
|
--cluster-file `pwd`/${clusters} \\
|
|
${reference} \\
|
|
--mei-refs ${mei_reference} \\
|
|
--out-name `pwd`/${prefix}
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
scramble: ${VERSION}
|
|
${blastdb_version}
|
|
END_VERSIONS
|
|
"""
|
|
}
|