mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
e7845e2472
* msisensor2: Add msisensor2 module * msisensor2/scan module added * msisensor2 tests added Changes: - tests added for msisensor2 from the msisensor2 github repo. No available tests from NF-Core test repo. Relates to #1976 * msisensor2 slight bump in stuff * msisensor2: Replaced spelling of 'tumour' with 'tumor' * msisensor2: fix linting, testing and containers Relates to #1976 Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
48 lines
1.7 KiB
Text
48 lines
1.7 KiB
Text
process MSISENSOR2_MSI {
|
|
tag "$meta.id"
|
|
label 'process_medium'
|
|
|
|
conda (params.enable_conda ? "bioconda::msisensor2=0.1" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/msisensor2:0.1--hd03093a_0':
|
|
'quay.io/biocontainers/msisensor2:0.1--hd03093a_0' }"
|
|
|
|
input:
|
|
tuple val(meta), path(tumor_bam), path(tumor_bam_index), path(normal_bam), path(normal_bam_index), path(intervals)
|
|
path scan
|
|
path(models, stageAs: "models/*")
|
|
|
|
output:
|
|
tuple val(meta), path("${prefix}") , emit: msi
|
|
tuple val(meta), path("${prefix}_dis") , emit: distribution
|
|
tuple val(meta), path("${prefix}_somatic"), emit: somatic
|
|
path "versions.yml" , emit: versions
|
|
|
|
when:
|
|
task.ext.when == null || task.ext.when
|
|
|
|
script:
|
|
def args = task.ext.args ?: ''
|
|
prefix = task.ext.prefix ?: "${meta.id}"
|
|
def scan_cmd = scan ? "-d $scan" : ""
|
|
def model_cmd = models ? "-M models/" : ""
|
|
def tumor_bam_cmd = tumor_bam ? "-t $tumor_bam" : ""
|
|
def normal_bam_cmd = normal_bam ? "-n $normal_bam" : ""
|
|
def interval_command = intervals ? "-e $intervals" : ""
|
|
"""
|
|
msisensor2 msi \\
|
|
-b ${task.cpus} \\
|
|
$args \\
|
|
$model_cmd \\
|
|
$scan_cmd \\
|
|
$interval_command \\
|
|
$tumor_bam_cmd \\
|
|
$normal_bam_cmd \\
|
|
-o $prefix
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
msisensor2: \$(echo \$(msisensor2 2> >(grep Version) | sed 's/Version: v//g'))
|
|
END_VERSIONS
|
|
"""
|
|
}
|