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1 process KMA_INDEX {
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2 tag "$meta.id"
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3 label 'process_nano'
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4
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5 module (params.enable_module ? "${params.swmodulepath}${params.fs}kma${params.fs}1.4.4" : null)
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6 conda (params.enable_conda ? "conda-forge::libgcc-ng bioconda::kma=1.4.3 conda-forge::coreutils" : null)
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7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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8 'https://depot.galaxyproject.org/singularity/kma:1.4.3--h7132678_1':
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9 'quay.io/biocontainers/kma:1.4.3--h7132678_1' }"
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10
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11 input:
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12 tuple val(meta), path(fasta)
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13
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14 output:
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15 tuple val(meta), path("${meta.id}_kma_idx"), emit: idx
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16 path "versions.yml" , emit: versions
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17
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18 when:
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19 task.ext.when == null || task.ext.when
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20
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21 script:
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22 def args = task.ext.args ?: ''
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23 def prefix = task.ext.prefix ?: "${meta.id}_kma_idx"
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24 def add_to_db = (meta.kmaindex_t_db ? "-t_db ${meta.kmaindex_t_db}" : '')
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25 """
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26 mkdir -p $prefix && cd $prefix || exit 1
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27 kma \\
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28 index \\
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29 $args \\
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30 $add_to_db \\
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31 -i ../$fasta \\
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32 -o $prefix
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33 cd .. || exit 1
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34
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35 cat <<-END_VERSIONS > versions.yml
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36 "${task.process}":
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37 kma: \$( kma -v | sed -e 's%KMA-%%' )
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38 END_VERSIONS
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39
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40 mkdirver=""
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41 cutver=""
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42
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43 if [ "${workflow.containerEngine}" != "null" ]; then
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44 mkdirver=\$( mkdir --help 2>&1 | sed -e '1!d; s/ (.*\$//' | cut -f1-2 -d' ' )
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45 cutver="\$mkdirver"
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46 else
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47 mkdirver=\$( mkdir --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
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48 cutver=\$( cut --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' )
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49 fi
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50
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51 cat <<-END_VERSIONS >> versions.yml
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52 mkdir: \$mkdirver
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53 cut: \$cutver
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54 cd: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' )
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55 END_VERSIONS
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56 """
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57 } |
