Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.7.0/modules/kma/index/main.nf @ 21:4ce0e079377d tip
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 12:01:00 -0400 |
| parents | 0e7a0053e4a6 |
| children |
| rev | line source |
|---|---|
| kkonganti@17 | 1 process KMA_INDEX { |
| kkonganti@17 | 2 tag "$meta.id" |
| kkonganti@17 | 3 label 'process_nano' |
| kkonganti@17 | 4 |
| kkonganti@17 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}kma${params.fs}1.4.4" : null) |
| kkonganti@17 | 6 conda (params.enable_conda ? "conda-forge::libgcc-ng bioconda::kma=1.4.3 conda-forge::coreutils" : null) |
| kkonganti@17 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@17 | 8 'https://depot.galaxyproject.org/singularity/kma:1.4.3--h7132678_1': |
| kkonganti@17 | 9 'quay.io/biocontainers/kma:1.4.3--h7132678_1' }" |
| kkonganti@17 | 10 |
| kkonganti@17 | 11 input: |
| kkonganti@17 | 12 tuple val(meta), path(fasta) |
| kkonganti@17 | 13 |
| kkonganti@17 | 14 output: |
| kkonganti@17 | 15 tuple val(meta), path("${meta.id}_kma_idx"), emit: idx |
| kkonganti@17 | 16 path "versions.yml" , emit: versions |
| kkonganti@17 | 17 |
| kkonganti@17 | 18 when: |
| kkonganti@17 | 19 task.ext.when == null || task.ext.when |
| kkonganti@17 | 20 |
| kkonganti@17 | 21 script: |
| kkonganti@17 | 22 def args = task.ext.args ?: '' |
| kkonganti@17 | 23 def prefix = task.ext.prefix ?: "${meta.id}_kma_idx" |
| kkonganti@17 | 24 def add_to_db = (meta.kmaindex_t_db ? "-t_db ${meta.kmaindex_t_db}" : '') |
| kkonganti@17 | 25 """ |
| kkonganti@17 | 26 mkdir -p $prefix && cd $prefix || exit 1 |
| kkonganti@17 | 27 kma \\ |
| kkonganti@17 | 28 index \\ |
| kkonganti@17 | 29 $args \\ |
| kkonganti@17 | 30 $add_to_db \\ |
| kkonganti@17 | 31 -i ../$fasta \\ |
| kkonganti@17 | 32 -o $prefix |
| kkonganti@17 | 33 cd .. || exit 1 |
| kkonganti@17 | 34 |
| kkonganti@17 | 35 cat <<-END_VERSIONS > versions.yml |
| kkonganti@17 | 36 "${task.process}": |
| kkonganti@17 | 37 kma: \$( kma -v | sed -e 's%KMA-%%' ) |
| kkonganti@17 | 38 END_VERSIONS |
| kkonganti@17 | 39 |
| kkonganti@17 | 40 mkdirver="" |
| kkonganti@17 | 41 cutver="" |
| kkonganti@17 | 42 |
| kkonganti@17 | 43 if [ "${workflow.containerEngine}" != "null" ]; then |
| kkonganti@17 | 44 mkdirver=\$( mkdir --help 2>&1 | sed -e '1!d; s/ (.*\$//' | cut -f1-2 -d' ' ) |
| kkonganti@17 | 45 cutver="\$mkdirver" |
| kkonganti@17 | 46 else |
| kkonganti@17 | 47 mkdirver=\$( mkdir --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' ) |
| kkonganti@17 | 48 cutver=\$( cut --version 2>&1 | sed '1!d; s/^.*(GNU coreutils//; s/) //;' ) |
| kkonganti@17 | 49 fi |
| kkonganti@17 | 50 |
| kkonganti@17 | 51 cat <<-END_VERSIONS >> versions.yml |
| kkonganti@17 | 52 mkdir: \$mkdirver |
| kkonganti@17 | 53 cut: \$cutver |
| kkonganti@17 | 54 cd: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' ) |
| kkonganti@17 | 55 END_VERSIONS |
| kkonganti@17 | 56 """ |
| kkonganti@17 | 57 } |