mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-15 14:13:09 +00:00
49 lines
2 KiB
Text
49 lines
2 KiB
Text
|
process SCRAMBLE_CLUSTERIDENTIFIER {
|
||
|
|
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(input), path(input_index)
|
||
|
|
path fasta
|
||
|
|
|
||
|
|
output:
|
||
|
|
tuple val(meta), path("*.clusters.txt") , emit: clusters
|
||
|
|
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.
|
||
|
|
|
||
|
|
// The tool does not contain a way to specify the reference file when using CRAM files.
|
||
|
|
// It just looks in the header of the CRAM file where the reference file is located,
|
||
|
|
// but that reference can't always be fetched since most test data is created on
|
||
|
|
// another machine. I had to find another way to specify the reference and I
|
||
|
|
// found that I could create an md5 cache of a specified fasta and supply it to
|
||
|
|
// the REF_PATH environment variable. This way the tool uses the correct reference.
|
||
|
|
// An issue has been made about this: https://github.com/GeneDx/scramble/issues/27
|
||
|
|
// The reference code is a placeholder until this issue has been fixed.
|
||
|
|
def reference = fasta ? "wget https://raw.githubusercontent.com/samtools/samtools/master/misc/seq_cache_populate.pl && perl seq_cache_populate.pl -root ./md5_ref ${fasta} && export REF_PATH=`pwd`/md5_ref/%2s/%2s/%s" : ""
|
||
|
|
"""
|
||
|
|
${reference}
|
||
|
|
|
||
|
|
cluster_identifier \\
|
||
|
|
${args} \\
|
||
|
|
${input} \\
|
||
|
|
> ${prefix}.clusters.txt
|
||
|
|
|
||
|
|
cat <<-END_VERSIONS > versions.yml
|
||
|
|
"${task.process}":
|
||
|
|
scramble: ${VERSION}
|
||
|
|
END_VERSIONS
|
||
|
|
"""
|
||
|
|
}
|