Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.7.0/modules/sourmash/search/main.nf @ 17:0e7a0053e4a6
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 10:42:02 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@17 | 1 process SOURMASH_SEARCH { |
| kkonganti@17 | 2 tag "$meta.id" |
| kkonganti@17 | 3 label 'process_micro' |
| kkonganti@17 | 4 |
| kkonganti@17 | 5 module (params.enable_module ? "${params.swmodulepath}${params.fs}sourmash${params.fs}4.6.1" : null) |
| kkonganti@17 | 6 conda (params.enable_conda ? "conda-forge::python bioconda::sourmash=4.6.1" : null) |
| kkonganti@17 | 7 container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@17 | 8 'https://depot.galaxyproject.org/singularity/sourmash:4.6.1--hdfd78af_0': |
| kkonganti@17 | 9 'quay.io/biocontainers/sourmash:4.6.1--hdfd78af_0' }" |
| kkonganti@17 | 10 |
| kkonganti@17 | 11 input: |
| kkonganti@17 | 12 tuple val(meta), path(signature), path(database) |
| kkonganti@17 | 13 val save_matches_sig |
| kkonganti@17 | 14 |
| kkonganti@17 | 15 output: |
| kkonganti@17 | 16 tuple val(meta), path("*.csv.gz") , emit: result , optional: true |
| kkonganti@17 | 17 tuple val(meta), path("*_scaffolded_genomic.fna.gz"), emit: genomes_fasta, optional: true |
| kkonganti@17 | 18 tuple val(meta), path("*_matches.sig.zip") , emit: matches , optional: true |
| kkonganti@17 | 19 path "*FAILED.txt" , emit: failed , optional: true |
| kkonganti@17 | 20 path "versions.yml" , emit: versions |
| kkonganti@17 | 21 |
| kkonganti@17 | 22 when: |
| kkonganti@17 | 23 task.ext.when == null || task.ext.when |
| kkonganti@17 | 24 |
| kkonganti@17 | 25 script: |
| kkonganti@17 | 26 def args = task.ext.args ?: '' |
| kkonganti@17 | 27 def args2 = task.ext.args2 ?: '' |
| kkonganti@17 | 28 def prefix = task.ext.prefix ?: "${meta.id}" |
| kkonganti@17 | 29 def matches = save_matches_sig ? "--save-matches ${prefix}_matches.sig.zip" : '' |
| kkonganti@17 | 30 def gd = params.tuspy_gd ? "-gd ${params.tuspy_gd}" : '' |
| kkonganti@17 | 31 |
| kkonganti@17 | 32 """ |
| kkonganti@17 | 33 sourmash search \\ |
| kkonganti@17 | 34 $args \\ |
| kkonganti@17 | 35 --output ${prefix}.csv.gz \\ |
| kkonganti@17 | 36 ${matches} \\ |
| kkonganti@17 | 37 ${signature} \\ |
| kkonganti@17 | 38 ${database} |
| kkonganti@17 | 39 |
| kkonganti@17 | 40 sourmash_filter_hits.py \\ |
| kkonganti@17 | 41 $args2 \\ |
| kkonganti@17 | 42 -csv ${prefix}.csv.gz |
| kkonganti@17 | 43 |
| kkonganti@17 | 44 gen_otf_genome.py \\ |
| kkonganti@17 | 45 $gd \\ |
| kkonganti@17 | 46 -op ${prefix} \\ |
| kkonganti@17 | 47 -txt ${prefix}_template_hits.txt |
| kkonganti@17 | 48 |
| kkonganti@17 | 49 cat <<-END_VERSIONS > versions.yml |
| kkonganti@17 | 50 "${task.process}": |
| kkonganti@17 | 51 sourmash: \$(echo \$(sourmash --version 2>&1) | sed 's/^sourmash //' ) |
| kkonganti@17 | 52 python: \$( python --version | sed 's/Python //g' ) |
| kkonganti@17 | 53 END_VERSIONS |
| kkonganti@17 | 54 """ |
| kkonganti@17 | 55 } |