cfsan_cronology: 0.1.0/modules/mash/screen/main.nf annotate

"planemo upload"

rev	line source
kkonganti@0	1 process MASH_SCREEN {
kkonganti@0	2 tag "$meta.id"
kkonganti@0	3 label 'process_micro'
kkonganti@0	4
kkonganti@0	5 module (params.enable_module ? "${params.swmodulepath}${params.fs}mash${params.fs}2.3" : null)
kkonganti@0	6 conda (params.enable_conda ? "conda-forge::capnproto conda-forge::gsl bioconda::mash=2.3" : null)
kkonganti@0	7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
kkonganti@0	8 'https://depot.galaxyproject.org/singularity/mash:2.3--he348c14_1':
kkonganti@0	9 'quay.io/biocontainers/mash:2.3--he348c14_1' }"
kkonganti@0	10
kkonganti@0	11 input:
kkonganti@0	12 tuple val(meta), path(query)
kkonganti@0	13
kkonganti@0	14 output:
kkonganti@0	15 tuple val(meta), path("*.screened"), emit: screened
kkonganti@0	16 path "versions.yml" , emit: versions
kkonganti@0	17
kkonganti@0	18 when:
kkonganti@0	19 task.ext.when == null \|\| task.ext.when
kkonganti@0	20
kkonganti@0	21 script:
kkonganti@0	22 def args = task.ext.args ?: ''
kkonganti@0	23 def prefix = task.ext.prefix ?: "${meta.id}"
kkonganti@0	24 def sequence_sketch = (meta.sequence_sketch ?: '')
kkonganti@0	25 """
kkonganti@0	26 mash \\
kkonganti@0	27 screen \\
kkonganti@0	28 $args \\
kkonganti@0	29 -p $task.cpus \\
kkonganti@0	30 $sequence_sketch \\
kkonganti@0	31 $query \\
kkonganti@0	32 > ${prefix}.screened
kkonganti@0	33
kkonganti@0	34 cat <<-END_VERSIONS > versions.yml
kkonganti@0	35 "${task.process}":
kkonganti@0	36 mash: \$( mash --version )
kkonganti@0	37 END_VERSIONS
kkonganti@0	38 """
kkonganti@0	39 }

Mercurial > repos > kkonganti > cfsan_cronology