nf-core_modules/modules/lima/main.nf
2021-12-24 11:32:30 +00:00

67 lines
2.7 KiB
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process LIMA {
tag "$meta.id"
label 'process_medium'
conda (params.enable_conda ? "bioconda::lima=2.2.0" : null)
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/lima:2.2.0--h9ee0642_0' :
'quay.io/biocontainers/lima:2.2.0--h9ee0642_0' }"
input:
tuple val(meta), path(ccs)
path primers
output:
tuple val(meta), path("*.counts") , emit: counts
tuple val(meta), path("*.report") , emit: report
tuple val(meta), path("*.summary"), emit: summary
path "versions.yml" , emit: versions
tuple val(meta), path("*.bam") , optional: true, emit: bam
tuple val(meta), path("*.bam.pbi") , optional: true, emit: pbi
tuple val(meta), path("*.{fa, fasta}") , optional: true, emit: fasta
tuple val(meta), path("*.{fa.gz, fasta.gz}"), optional: true, emit: fastagz
tuple val(meta), path("*.fastq") , optional: true, emit: fastq
tuple val(meta), path("*.fastq.gz") , optional: true, emit: fastqgz
tuple val(meta), path("*.xml") , optional: true, emit: xml
tuple val(meta), path("*.json") , optional: true, emit: json
tuple val(meta), path("*.clips") , optional: true, emit: clips
tuple val(meta), path("*.guess") , optional: true, emit: guess
script:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if( "$ccs" == "${prefix}.bam" ) error "Input and output names are the same, set prefix in module configuration"
if( "$ccs" == "${prefix}.fasta" ) error "Input and output names are the same, set prefix in module configuration"
if( "$ccs" == "${prefix}.fasta.gz" ) error "Input and output names are the same, set prefix in module configuration"
if( "$ccs" == "${prefix}.fastq" ) error "Input and output names are the same, set prefix in module configuration"
if( "$ccs" == "${prefix}.fastq.gz" ) error "Input and output names are the same, set prefix in module configuration"
"""
OUT_EXT=""
if [[ $ccs =~ bam\$ ]]; then
OUT_EXT="bam"
elif [[ $ccs =~ fasta\$ ]]; then
OUT_EXT="fasta"
elif [[ $ccs =~ fasta.gz\$ ]]; then
OUT_EXT="fasta.gz"
elif [[ $ccs =~ fastq\$ ]]; then
OUT_EXT="fastq"
elif [[ $ccs =~ fastq.gz\$ ]]; then
OUT_EXT="fastq.gz"
fi
lima \\
$ccs \\
$primers \\
$prefix.\$OUT_EXT \\
-j $task.cpus \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
lima: \$( lima --version | sed 's/lima //g' | sed 's/ (.\\+//g' )
END_VERSIONS
"""
}