Mercurial > repos > kkonganti > cfsan_centriflaken
annotate 0.4.2/modules/seqtk/seq/main.nf @ 143:620bffa66bbb tip
planemo upload
| author | kkonganti |
|---|---|
| date | Thu, 11 Jul 2024 14:48:07 -0400 |
| parents | 52045ea4679d |
| children |
| rev | line source |
|---|---|
| kkonganti@105 | 1 process SEQTK_SEQ { |
| kkonganti@105 | 2 tag "$meta.id" |
| kkonganti@105 | 3 label 'process_mem_low' |
| kkonganti@105 | 4 |
| kkonganti@105 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}seqtk${params.fs}1.3-r106" : null) |
| kkonganti@105 | 6 conda (params.enable_conda ? "bioconda::seqtk=1.3 conda-forge::gzip" : null) |
| kkonganti@105 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@105 | 8 'https://depot.galaxyproject.org/singularity/seqtk:1.3--h5bf99c6_3' : |
| kkonganti@105 | 9 'quay.io/biocontainers/seqtk:1.3--h5bf99c6_3' }" |
| kkonganti@105 | 10 |
| kkonganti@105 | 11 input: |
| kkonganti@105 | 12 tuple val(meta), path(fastx) |
| kkonganti@105 | 13 |
| kkonganti@105 | 14 output: |
| kkonganti@105 | 15 tuple val(meta), path("*.gz"), emit: fastx |
| kkonganti@105 | 16 path "versions.yml" , emit: versions |
| kkonganti@105 | 17 |
| kkonganti@105 | 18 when: |
| kkonganti@105 | 19 task.ext.when == null || task.ext.when |
| kkonganti@105 | 20 |
| kkonganti@105 | 21 script: |
| kkonganti@105 | 22 def args = task.ext.args ?: '' |
| kkonganti@105 | 23 def prefix = task.ext.prefix ?: "${meta.id}" |
| kkonganti@105 | 24 |
| kkonganti@105 | 25 def extension = "fastq" |
| kkonganti@105 | 26 if ("$fastx" ==~ /.+\.fasta|.+\.fasta.gz|.+\.fa|.+\.fa.gz|.+\.fas|.+\.fas.gz|.+\.fna|.+\.fna.gz/ || "$args" ==~ /\-[aA]/ ) { |
| kkonganti@105 | 27 extension = "fasta" |
| kkonganti@105 | 28 } |
| kkonganti@105 | 29 """ |
| kkonganti@105 | 30 seqtk \\ |
| kkonganti@105 | 31 seq \\ |
| kkonganti@105 | 32 $args \\ |
| kkonganti@105 | 33 $fastx | \\ |
| kkonganti@105 | 34 gzip -c > ${prefix}.seqtk-seq.${task.index}.${extension}.gz |
| kkonganti@105 | 35 |
| kkonganti@105 | 36 cat <<-END_VERSIONS > versions.yml |
| kkonganti@105 | 37 "${task.process}": |
| kkonganti@105 | 38 seqtk: \$(echo \$(seqtk 2>&1) | sed 's/^.*Version: //; s/ .*\$//') |
| kkonganti@105 | 39 gzip: \$( echo \$(gzip --version 2>&1) | sed 's/^.*(gzip) //; s/gzip //; s/ Copyright.*\$//' ) |
| kkonganti@105 | 40 END_VERSIONS |
| kkonganti@105 | 41 """ |
| kkonganti@105 | 42 } |