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Update taxpasta/merge to version 0.2.0 and add taxonomy argument
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parent
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commit
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5 changed files with 16 additions and 5 deletions
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@ -543,7 +543,12 @@ process {
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}
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withName: TAXPASTA_MERGE {
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ext.args = { "-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}" }
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ext.args = {
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[
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"-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}",
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params.taxpasta_add_taxonomy ? "--taxonomy" : "",
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].join(' ').trim()
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}
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publishDir = [
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path: { "${params.outdir}/taxpasta/" },
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mode: params.publish_dir_mode,
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@ -209,7 +209,7 @@
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},
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"taxpasta/merge": {
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"branch": "master",
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"git_sha": "74ab450ed05e034d049c00f6e2853de2c31594b4",
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"git_sha": "fe58454add6225d2b7468e6d72a3a1f6a3149638",
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"installed_by": ["modules"]
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},
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"untar": {
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6
modules/nf-core/taxpasta/merge/main.nf
generated
6
modules/nf-core/taxpasta/merge/main.nf
generated
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@ -2,10 +2,10 @@ process TAXPASTA_MERGE {
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tag "$meta.id"
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label 'process_single'
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conda "bioconda::taxpasta=0.1.1"
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conda "bioconda::taxpasta=0.2.0"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/taxpasta:0.1.1--pyhdfd78af_0':
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'quay.io/biocontainers/taxpasta:0.1.1--pyhdfd78af_0' }"
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'https://depot.galaxyproject.org/singularity/taxpasta:0.2.0--pyhdfd78af_0':
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'quay.io/biocontainers/taxpasta:0.2.0--pyhdfd78af_0' }"
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input:
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@ -157,6 +157,7 @@ params {
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// profile standardisation
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run_profile_standardisation = false
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standardisation_taxpasta_format = 'tsv'
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taxpasta_add_taxonomy = false
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standardisation_motus_generatebiom = false
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}
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@ -516,6 +516,11 @@
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"fa_icon": "fas fa-file",
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"description": "The desired output format.",
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"enum": ["tsv", "csv", "arrow", "parquet", "biom"]
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},
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"taxpasta_add_taxonomy": {
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"type": "boolean",
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"description": "The path to a directory containing taxdump files.",
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"help_text": "At least nodes.dmp and names.dmp are required. A merged.dmp file is optional."
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}
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},
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"fa_icon": "fas fa-chart-line"
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