nf-core_modules/modules/chromap/index/main.nf
Jose Espinosa-Carrasco 62da45b0e1
Bump chromap version 0.2.0 (#1374)
* Bump chromap version 0.2.0

* Temporary use the docker container until singularity container becomes available

* Temporary use the docker container until singularity container available

* Remove empty lines

* Update singularity container after became available
2022-03-10 09:23:45 +01:00

36 lines
909 B
Text

process CHROMAP_INDEX {
tag '$fasta'
label 'process_medium'
conda (params.enable_conda ? "bioconda::chromap=0.2.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/chromap:0.2.0--hd03093a_1' :
'quay.io/biocontainers/chromap:0.2.0--hd03093a_1' }"
input:
path fasta
output:
path "*.index" , emit: index
path "versions.yml", emit: versions
when:
task.ext.when == null || task.ext.when
script:
def args = task.ext.args ?: ''
def prefix = fasta.baseName
"""
chromap \\
-i \\
$args \\
-t $task.cpus \\
-r $fasta \\
-o ${prefix}.index
cat <<-END_VERSIONS > versions.yml
"${task.process}":
chromap: \$(echo \$(chromap --version 2>&1))
END_VERSIONS
"""
}