Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.4.0/modules/spades/assemble/main.nf @ 101:ce6d9548fe89

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"planemo upload"
author kkonganti
date Thu, 04 Aug 2022 10:45:55 -0400
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100:9d9537c907bd 101:ce6d9548fe89
1 process SPADES_ASSEMBLE {
2 tag "$meta.id"
3 label 'process_higher'
4
5 module (params.enable_module ? "${params.swmodulepath}${params.fs}spades${params.fs}3.15.3" : null)
6 conda (params.enable_conda ? 'bioconda::spades=3.15.3' : null)
7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
8 'https://depot.galaxyproject.org/singularity/spades:3.15.3--h95f258a_0' :
9 'quay.io/biocontainers/spades:3.15.3--h95f258a_0' }"
10
11 input:
12 tuple val(meta), path(illumina), path(pacbio), path(nanopore)
13
14 output:
15 path "${meta.id}${params.fs}*"
16 tuple val(meta), path("${meta.id}${params.fs}scaffolds.fasta"), emit: assembly, optional: true
17 tuple val(meta), path("${meta.id}${params.fs}spades.log") , emit: log
18 path "versions.yml" , emit: versions
19
20 when:
21 task.ext.when == null || task.ext.when
22
23 script:
24 def args = task.ext.args ?: ''
25 def prefix = task.ext.prefix ?: "${meta.id}"
26 def maxmem = task.memory ? "--memory ${task.memory.toGiga()}" : ""
27 def illumina_reads = illumina ? ( meta.single_end ? "-s $illumina" : "-1 ${illumina[0]} -2 ${illumina[1]}" ) : ""
28 def pacbio_reads = !(pacbio.simpleName ==~ 'dummy_file.*') ? "--pacbio $pacbio" : ""
29 def nanopore_reads = !(nanopore.simpleName ==~ 'dummy_file.*') ? "--nanopore $nanopore" : ""
30 def custom_hmms = params.spades_hmm ? "--custom-hmms ${params.spades_hmm}" : ""
31 """
32 spades.py \\
33 $args \\
34 --threads $task.cpus \\
35 $maxmem \\
36 $custom_hmms \\
37 $illumina_reads \\
38 $pacbio_reads \\
39 $nanopore_reads \\
40 -o ${prefix}
41
42 cat <<-END_VERSIONS > versions.yml
43 "${task.process}":
44 spades: \$(spades.py --version 2>&1 | sed 's/^.*SPAdes genome assembler v//; s/ .*\$//')
45 END_VERSIONS
46 """
47 }