mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-10 20:23:10 +00:00
37c6d4a1a1
* first commit
* single taxon input
* added .tsv output
* input: single taxon or file with taxon identifiers
* updated input and output
* removed wrong tool description
* added tests
* ext.args = '-l -b'
* fixed wrong input names
* updated test file
* Update modules/goat/taxonsearch/main.nf
simple version output
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
* removed 'NO_FILE' from input definition
* added ! in if statement
* optional input: empty list
* successful updated test
* added test with file
* remove blank spaces in include {}
* added test with taxa file
Co-authored-by: Matthieu Muffato <mm49@sanger.ac.uk>
36 lines
1.2 KiB
Text
36 lines
1.2 KiB
Text
process GOAT_TAXONSEARCH {
|
|
tag "$meta.id"
|
|
label 'process_low'
|
|
|
|
conda (params.enable_conda ? "bioconda::goat=0.2.0" : null)
|
|
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
|
|
'https://depot.galaxyproject.org/singularity/goat:0.2.0--h92d785c_0':
|
|
'quay.io/biocontainers/goat:0.2.0--h92d785c_0' }"
|
|
|
|
input:
|
|
tuple val(meta), val(taxon), path(taxa_file)
|
|
|
|
output:
|
|
tuple val(meta), path("*.tsv"), emit: taxonsearch
|
|
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}"
|
|
input = taxa_file ? "-f ${taxa_file}" : "-t ${taxon}"
|
|
if (!taxon && !taxa_file) error "No input. Valid input: single taxon identifier or a .txt file with identifiers"
|
|
if (taxon && taxa_file ) error "Only one input is required: a single taxon identifier or a .txt file with identifiers"
|
|
"""
|
|
goat-cli taxon search \\
|
|
$args \\
|
|
$input > ${prefix}.tsv
|
|
|
|
cat <<-END_VERSIONS > versions.yml
|
|
"${task.process}":
|
|
goat: \$(goat-cli --version | cut -d' ' -f2)
|
|
END_VERSIONS
|
|
"""
|
|
}
|