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