Mercurial > repos > kkonganti > cfsan_centriflaken

comparison 0.2.1/modules/spades/assemble/main.nf @ 37:a047ee0e34ae

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"planemo upload"
author kkonganti
date Wed, 29 Jun 2022 19:24:35 -0400
parents 77494b0fa3c7
children
comparison
equal deleted inserted replaced
36:1d6557e7db72 37:a047ee0e34ae
21 task.ext.when == null || task.ext.when 21 task.ext.when == null || task.ext.when
22 22
23 script: 23 script:
24 def args = task.ext.args ?: '' 24 def args = task.ext.args ?: ''
25 def prefix = task.ext.prefix ?: "${meta.id}" 25 def prefix = task.ext.prefix ?: "${meta.id}"
26 def maxmem = task.memory.toGiga() 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]}" ) : "" 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" : "" 28 def pacbio_reads = !(pacbio.simpleName ==~ 'dummy_file.*') ? "--pacbio $pacbio" : ""
29 def nanopore_reads = !(nanopore.simpleName ==~ 'dummy_file.*') ? "--nanopore $nanopore" : "" 29 def nanopore_reads = !(nanopore.simpleName ==~ 'dummy_file.*') ? "--nanopore $nanopore" : ""
30 def custom_hmms = params.spades_hmm ? "--custom-hmms ${params.spades_hmm}" : "" 30 def custom_hmms = params.spades_hmm ? "--custom-hmms ${params.spades_hmm}" : ""
31 """ 31 """
32 spades.py \\ 32 spades.py \\
33 $args \\ 33 $args \\
34 --threads $task.cpus \\ 34 --threads $task.cpus \\
35 --memory $maxmem \\ 35 $maxmem \\
36 $custom_hmms \\ 36 $custom_hmms \\
37 $illumina_reads \\ 37 $illumina_reads \\
38 $pacbio_reads \\ 38 $pacbio_reads \\
39 $nanopore_reads \\ 39 $nanopore_reads \\
40 -o ${prefix} 40 -o ${prefix}