Mercurial > repos > kkonganti > cfsan_bettercallsal
comparison 0.6.1/modules/sourmash/sig/kmers/main.nf @ 11:749faef1caa9
"planemo upload"
| author | kkonganti |
|---|---|
| date | Tue, 05 Sep 2023 11:51:40 -0400 |
| parents | |
| children |
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| 10:1b9de878b04a | 11:749faef1caa9 |
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| 1 process SOURMASH_SIG_KMERS { | |
| 2 tag "$meta.id" | |
| 3 label 'process_micro' | |
| 4 | |
| 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}sourmash${params.fs}4.6.1" : null) | |
| 6 conda (params.enable_conda ? "conda-forge::python bioconda::sourmash=4.6.1" : null) | |
| 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | |
| 8 'https://depot.galaxyproject.org/singularity/sourmash:4.6.1--hdfd78af_0' : | |
| 9 'quay.io/biocontainers/sourmash:4.6.1--hdfd78af_0' }" | |
| 10 | |
| 11 input: | |
| 12 tuple val(meta), path(sig_or_seq), path(sequence) | |
| 13 | |
| 14 output: | |
| 15 tuple val(meta), path("*.csv") , emit: signatures, optional: true | |
| 16 tuple val(meta), path("*.fasta"), emit: extracted_fasta, optional: true | |
| 17 path "versions.yml" , emit: versions | |
| 18 | |
| 19 when: | |
| 20 task.ext.when == null || task.ext.when | |
| 21 | |
| 22 script: | |
| 23 // required defaults for the tool to run, but can be overridden | |
| 24 def args = task.ext.args ?: '' | |
| 25 def is_seq = "${sig_or_seq.baseName.findAll(/(?i)\.(fa|fasta|fna)\.{0,1}(gz){0,1}$/).size()}" | |
| 26 def save_kmers = (params.sourmashsigkmers_save_kmers ? "--save-kmers ${meta.id}.sm.kmers.csv" : '') | |
| 27 def save_seqs = (params.sourmashsigkmers_save_seqs ? "--save-sequences ${meta.id}.sm.seq.fasta" : '') | |
| 28 def sketch_mode = (params.sourmashsketch_mode ?: 'dna') | |
| 29 def sketch_p = (params.sourmashsketch_p ?: "abund,scaled=1000,k=71") | |
| 30 def prefix = task.ext.prefix ?: "${meta.id}" | |
| 31 """ | |
| 32 db_sig="${sig_or_seq}" | |
| 33 if [[ $is_seq -ge 1 ]]; then | |
| 34 db_sig="${prefix}.db.sig" | |
| 35 sourmash sketch \\ | |
| 36 $sketch_mode \\ | |
| 37 -p '$sketch_p' \\ | |
| 38 --output \$db_sig \\ | |
| 39 $sig_or_seq | |
| 40 fi | |
| 41 | |
| 42 sourmash signature kmers \\ | |
| 43 $args \\ | |
| 44 $save_kmers \\ | |
| 45 $save_seqs \\ | |
| 46 --signatures \$db_sig \\ | |
| 47 --sequences $sequence | |
| 48 | |
| 49 cat <<-END_VERSIONS > versions.yml | |
| 50 "${task.process}": | |
| 51 sourmash: \$(echo \$(sourmash --version 2>&1) | sed 's/^sourmash //' ) | |
| 52 bash: \$( bash --version 2>&1 | sed '1!d; s/^.*version //; s/ (.*\$//' ) | |
| 53 END_VERSIONS | |
| 54 """ | |
| 55 } |