nf-core_modules/modules/cnvpytor/callcnvs/main.nf
Sima Rahimi 86ac223916
Cnvpytor (#1297)
* Added cnvpytor/importreaddepth module

* Corrected process name in meta.yml file

* added -chrom argument

* space correction

* Added complementary info

* fixed typo

* md5sum added

* modified the module to work on cram files as well

* Added cnvpytor/histogram module and test files

* Added cnvpytor/partition module and test files

* added cnvpytor/callcnvs module and tests

* modified by new modules

* Added test file and fixed input path in modules

* added when block

* little fixes

* skip tracking test.yml

* removed changes to test if conflicts get resolved

* updated outfile name

* corrected the version.yml content
2022-03-15 10:20:46 +01:00

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Text

process CNVPYTOR_CALLCNVS {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::cnvpytor=1.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/cnvpytor:A1.0--py39h6a678da_2':
'quay.io/biocontainers/cnvpytor:1.0--py39h6a678da_2' }"
input:
tuple val(meta), path(pytor)
output:
tuple val(meta), path("*.tsv"), emit: cnvs
path "versions.yml" , emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: '1000'
def prefix = task.ext.prefix ?: "${meta.id}"
"""
cnvpytor \\
-root $pytor \\
-call $args > ${prefix}.tsv
cat <<-END_VERSIONS > versions.yml
"${task.process}":
cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
END_VERSIONS
"""
}