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1 process FLYE_ASSEMBLE {
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2 tag "$meta.id"
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3 label 'process_medium'
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4 // errorStrategy 'ignore'
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5
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6 module (params.enable_module ? "${params.swmodulepath}${params.fs}flye${params.fs}2.9" : null)
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7 conda (params.enable_conda ? "bioconda::flye=2.9.0" : null)
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8 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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9 'https://depot.galaxyproject.org/singularity/flye:2.9--py38hf4f3596_1' :
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10 'quay.io/biocontainers/flye:2.9--py38hf4f3596_1' }"
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11
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12 input:
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13 tuple val(meta), path(reads)
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14
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15 output:
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16 path "${meta.id}${params.fs}*"
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17 tuple val(meta), path("${meta.id}${params.fs}assembly.fasta"), emit: assembly, optional: true
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18 path "versions.yml" , emit: versions
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19
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20 when:
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21 task.ext.when == null || task.ext.when
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22
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23 script:
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24 def args = task.ext.args ?: ''
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25 """
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26 reads_platform=\$( echo "$args" | grep -E -o '(--nano|--pacbio)-(raw|corr|hq|hifi)' )
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27 flye \\
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28 \$(echo "$args" | sed -e "s/\$reads_platform//") \\
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29 -t $task.cpus \\
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30 --out-dir "${meta.id}" \\
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31 \$reads_platform \\
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32 $reads
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33
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34 cat <<-END_VERSIONS > versions.yml
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35 "${task.process}":
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36 flye: \$( flye --version )
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37 END_VERSIONS
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38
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39 grepver=""
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40
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41 if [ "${workflow.containerEngine}" != "null" ]; then
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42 grepver=\$( grep --help 2>&1 | sed -e '1!d; s/ (.*\$//' )
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43 else
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44 grepver=\$( echo \$( grep --version 2>&1 ) | sed 's/^.*(GNU grep) //; s/ Copyright.*\$//' )
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45 fi
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46
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47 cat <<-END_VERSIONS >> versions.yml
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48 grep: \$grepver
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49 END_VERSIONS
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50 """
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51 } |
