Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.7.0/modules/sourmash/sketch/main.nf @ 20:133571bf891f
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 11:42:00 -0400 |
| parents | 0e7a0053e4a6 |
| children |
| rev | line source |
|---|---|
| kkonganti@17 | 1 process SOURMASH_SKETCH { |
| 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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? |
| kkonganti@17 | 8 'https://depot.galaxyproject.org/singularity/sourmash:4.6.1--hdfd78af_0': |
| kkonganti@17 | 9 'quay.io/biocontainers/sourmash:4.6.1--hdfd78af_0' }" |
| kkonganti@17 | 10 |
| kkonganti@17 | 11 input: |
| kkonganti@17 | 12 tuple val(meta), path(sequence), path(database) |
| kkonganti@17 | 13 |
| kkonganti@17 | 14 output: |
| kkonganti@17 | 15 tuple val(meta), path("*.query.sig"), path("*.db.sig"), emit: signatures |
| kkonganti@17 | 16 path "versions.yml" , emit: versions |
| kkonganti@17 | 17 |
| kkonganti@17 | 18 when: |
| kkonganti@17 | 19 task.ext.when == null || task.ext.when |
| kkonganti@17 | 20 |
| kkonganti@17 | 21 script: |
| kkonganti@17 | 22 // required defaults for the tool to run, but can be overridden |
| kkonganti@17 | 23 def args = task.ext.args ?: '' |
| kkonganti@17 | 24 def args_query |
| kkonganti@17 | 25 def prefix = task.ext.prefix ?: "${meta.id}" |
| kkonganti@17 | 26 """ |
| kkonganti@17 | 27 sourmash sketch \\ |
| kkonganti@17 | 28 ${args.toString().replace('--singleton', '')} \\ |
| kkonganti@17 | 29 --output "${prefix}.query.pre" \\ |
| kkonganti@17 | 30 $sequence |
| kkonganti@17 | 31 |
| kkonganti@17 | 32 sourmash signature rename \\ |
| kkonganti@17 | 33 --${args.toString().replaceAll(/\s+\-p.*/, '')} \\ |
| kkonganti@17 | 34 -o "${prefix}.query.sig" \\ |
| kkonganti@17 | 35 "${prefix}.query.pre" \\ |
| kkonganti@17 | 36 ${prefix} |
| kkonganti@17 | 37 |
| kkonganti@17 | 38 sourmash sketch \\ |
| kkonganti@17 | 39 $args \\ |
| kkonganti@17 | 40 --output "${prefix}.db.sig" \\ |
| kkonganti@17 | 41 $database |
| kkonganti@17 | 42 |
| kkonganti@17 | 43 cat <<-END_VERSIONS > versions.yml |
| kkonganti@17 | 44 "${task.process}": |
| kkonganti@17 | 45 sourmash: \$(echo \$(sourmash --version 2>&1) | sed 's/^sourmash //' ) |
| kkonganti@17 | 46 END_VERSIONS |
| kkonganti@17 | 47 """ |
| kkonganti@17 | 48 } |