nf-core_modules/software/minimap2/index/main.nf
Harshil Patel 466ab67808
Fixes for nanoseq modules (#479)
* Fix minimap2 index module

* Fix minimap2 index tests

* Fix graphmap2 index module

* Fix graphmap2 module

* Fix ECLint

* Fix bedtools bamtobed module

* Fix tests for bedtools bamtobed module

* Add tag for graphmap2 align module

* Fix EClint

* Fix qcat module

* Add md5sum for graphmap2/align module

* Remove non-started test data file

* Remove md5sum for graphmap2 align
2021-04-30 15:57:43 +01:00

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
options = initOptions(params.options)
process MINIMAP2_INDEX {
label 'process_medium'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:[:], publish_by_meta:['']) }
conda (params.enable_conda ? "bioconda::minimap2=2.17" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/minimap2:2.17--hed695b0_3"
} else {
container "quay.io/biocontainers/minimap2:2.17--hed695b0_3"
}
input:
path fasta
output:
path "*.mmi" , emit: index
path "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
"""
minimap2 \\
-t $task.cpus \\
-d ${fasta.baseName}.mmi \\
$options.args \\
$fasta
echo \$(minimap2 --version 2>&1) > ${software}.version.txt
"""
}