Mercurial > repos > kkonganti > cfsan_cronology
annotate 0.2.0/modules/shovill/main.nf @ 11:a5f31c44f8c9
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 16:11:44 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 process SHOVILL { |
| kkonganti@11 | 2 tag "$meta.id" |
| kkonganti@11 | 3 label 'process_low' |
| kkonganti@11 | 4 |
| kkonganti@11 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}shovill${params.fs}1.1.0" : null) |
| kkonganti@11 | 6 conda (params.enable_conda ? "bioconda::shovill=1.1.0 conda-forge::pigz" : null) |
| kkonganti@11 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@11 | 8 'https://depot.galaxyproject.org/singularity/shovill:1.1.0--0' : |
| kkonganti@11 | 9 'quay.io/biocontainers/shovill:1.1.0--0' }" |
| kkonganti@11 | 10 |
| kkonganti@11 | 11 input: |
| kkonganti@11 | 12 tuple val(meta), path(reads) |
| kkonganti@11 | 13 |
| kkonganti@11 | 14 output: |
| kkonganti@11 | 15 tuple val(meta), path("${prefix}${params.fs}contigs.fa") , emit: contigs |
| kkonganti@11 | 16 tuple val(meta), path("${prefix}${params.fs}shovill.corrections") , emit: corrections |
| kkonganti@11 | 17 tuple val(meta), path("${prefix}${params.fs}shovill.log") , emit: log |
| kkonganti@11 | 18 tuple val(meta), path("${prefix}${params.fs}{skesa,spades,megahit,velvet}.fasta"), emit: raw_contigs |
| kkonganti@11 | 19 tuple val(meta), path("${prefix}${params.fs}contigs.{fastg,gfa,LastGraph}") , emit: gfa, optional: true |
| kkonganti@11 | 20 path "versions.yml" , emit: versions |
| kkonganti@11 | 21 |
| kkonganti@11 | 22 when: |
| kkonganti@11 | 23 task.ext.when == null || task.ext.when |
| kkonganti@11 | 24 |
| kkonganti@11 | 25 script: |
| kkonganti@11 | 26 def args = task.ext.args ?: '' |
| kkonganti@11 | 27 def memory = (task.memory ? task.memory.toGiga() : 16) |
| kkonganti@11 | 28 prefix = (task.ext.prefix ?: meta.id) |
| kkonganti@11 | 29 """ |
| kkonganti@11 | 30 shovill \\ |
| kkonganti@11 | 31 --R1 ${reads[0]} \\ |
| kkonganti@11 | 32 --R2 ${reads[1]} \\ |
| kkonganti@11 | 33 $args \\ |
| kkonganti@11 | 34 --tmpdir ${prefix}${params.fs}tmp \\ |
| kkonganti@11 | 35 --cpus $task.cpus \\ |
| kkonganti@11 | 36 --ram $memory \\ |
| kkonganti@11 | 37 --outdir $prefix \\ |
| kkonganti@11 | 38 --force |
| kkonganti@11 | 39 |
| kkonganti@11 | 40 cat <<-END_VERSIONS > versions.yml |
| kkonganti@11 | 41 "${task.process}": |
| kkonganti@11 | 42 shovill: \$(echo \$(shovill --version 2>&1) | sed 's/^.*shovill //') |
| kkonganti@11 | 43 END_VERSIONS |
| kkonganti@11 | 44 """ |
| kkonganti@11 | 45 } |