Mercurial > repos > kkonganti > hfp_nowayout
comparison 0.5.0/modules/sourmash/gather/main.nf @ 0:97cd2f532efe
planemo upload
| author | kkonganti |
|---|---|
| date | Mon, 31 Mar 2025 14:50:40 -0400 |
| parents | |
| children |
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| -1:000000000000 | 0:97cd2f532efe |
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| 1 process SOURMASH_GATHER { | |
| 2 tag "$meta.id" | |
| 3 label 'process_nano' | |
| 4 | |
| 5 module (params.enable_module ? "${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 "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? | |
| 8 'https://depot.galaxyproject.org/singularity/sourmash:4.6.1--hdfd78af_0': | |
| 9 'quay.io/biocontainers/sourmash:4.6.1--hdfd78af_0' }" | |
| 10 | |
| 11 input: | |
| 12 tuple val(meta), path(signature), path(database) | |
| 13 val save_unassigned | |
| 14 val save_matches_sig | |
| 15 val save_prefetch | |
| 16 val save_prefetch_csv | |
| 17 | |
| 18 output: | |
| 19 tuple val(meta), path("*_hits.csv") , emit: result , optional: true | |
| 20 tuple val(meta), path("*_unassigned.sig.zip"), emit: unassigned , optional: true | |
| 21 tuple val(meta), path("*_matches.sig.zip") , emit: matches , optional: true | |
| 22 tuple val(meta), path("*_prefetch.sig.zip") , emit: prefetch , optional: true | |
| 23 tuple val(meta), path("*_prefetch.csv.gz") , emit: prefetchcsv , optional: true | |
| 24 tuple val(meta), path("*FAILED.txt") , emit: failed , optional: true | |
| 25 path "versions.yml" , emit: versions | |
| 26 | |
| 27 when: | |
| 28 task.ext.when == null || task.ext.when | |
| 29 | |
| 30 script: | |
| 31 def args = task.ext.args ?: '' | |
| 32 def args2 = task.ext.args2 ?: '' | |
| 33 def prefix = task.ext.prefix ?: "${meta.id}" | |
| 34 def unassigned = save_unassigned ? "--output-unassigned ${prefix}_unassigned.sig.zip" : '' | |
| 35 def matches = save_matches_sig ? "--save-matches ${prefix}_matches.sig.zip" : '' | |
| 36 def prefetch = save_prefetch ? "--save-prefetch ${prefix}_prefetch.sig.zip" : '' | |
| 37 def prefetchcsv = save_prefetch_csv ? "--save-prefetch-csv ${prefix}_prefetch.csv.gz" : '' | |
| 38 | |
| 39 """ | |
| 40 sourmash gather \\ | |
| 41 $args \\ | |
| 42 --output ${prefix}.csv.gz \\ | |
| 43 ${unassigned} \\ | |
| 44 ${matches} \\ | |
| 45 ${prefetch} \\ | |
| 46 ${prefetchcsv} \\ | |
| 47 ${signature} \\ | |
| 48 ${database} | |
| 49 | |
| 50 sourmash_filter_hits.py \\ | |
| 51 $args2 \\ | |
| 52 -csv ${prefix}.csv.gz | |
| 53 | |
| 54 cat <<-END_VERSIONS > versions.yml | |
| 55 "${task.process}": | |
| 56 sourmash: \$(echo \$(sourmash --version 2>&1) | sed 's/^sourmash //' ) | |
| 57 python: \$( python --version | sed 's/Python //g' ) | |
| 58 END_VERSIONS | |
| 59 """ | |
| 60 } |