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Update taxpasta/merge to version 0.2.0 and add taxonomy argument

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sofstam 2023-02-24 11:44:07 +01:00
parent 78c2d275e6
commit 5a6fcf1f42
5 changed files with 16 additions and 5 deletions
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7
conf/modules.config
View file

@ -543,7 +543,12 @@ process {
} }
withName: TAXPASTA_MERGE { withName: TAXPASTA_MERGE {
ext.args = { "-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}" } ext.args = {
[
"-p ${meta.tool} -o ${meta.tool}_${meta.id}.${params.standardisation_taxpasta_format}",
params.taxpasta_add_taxonomy ? "--taxonomy" : "",
].join(' ').trim()
}
publishDir = [ publishDir = [
path: { "${params.outdir}/taxpasta/" }, path: { "${params.outdir}/taxpasta/" },
mode: params.publish_dir_mode, mode: params.publish_dir_mode,

2
modules.json
View file

@ -209,7 +209,7 @@
}, },
"taxpasta/merge": { "taxpasta/merge": {
"branch": "master", "branch": "master",
"git_sha": "74ab450ed05e034d049c00f6e2853de2c31594b4", "git_sha": "fe58454add6225d2b7468e6d72a3a1f6a3149638",
"installed_by": ["modules"] "installed_by": ["modules"]
}, },
"untar": { "untar": {

6
modules/nf-core/taxpasta/merge/main.nf generated
View file

@ -2,10 +2,10 @@ process TAXPASTA_MERGE {
tag "$meta.id" tag "$meta.id"
label 'process_single' label 'process_single'
conda "bioconda::taxpasta=0.1.1" conda "bioconda::taxpasta=0.2.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/taxpasta:0.1.1--pyhdfd78af_0': 'https://depot.galaxyproject.org/singularity/taxpasta:0.2.0--pyhdfd78af_0':
'quay.io/biocontainers/taxpasta:0.1.1--pyhdfd78af_0' }" 'quay.io/biocontainers/taxpasta:0.2.0--pyhdfd78af_0' }"
input: input:

1
nextflow.config
View file

@ -157,6 +157,7 @@ params {
// profile standardisation // profile standardisation
run_profile_standardisation = false run_profile_standardisation = false
standardisation_taxpasta_format = 'tsv' standardisation_taxpasta_format = 'tsv'
taxpasta_add_taxonomy = false
standardisation_motus_generatebiom = false standardisation_motus_generatebiom = false
} }

5
nextflow_schema.json
View file

@ -516,6 +516,11 @@
"fa_icon": "fas fa-file", "fa_icon": "fas fa-file",
"description": "The desired output format.", "description": "The desired output format.",
"enum": ["tsv", "csv", "arrow", "parquet", "biom"] "enum": ["tsv", "csv", "arrow", "parquet", "biom"]
},
"taxpasta_add_taxonomy": {
"type": "boolean",
"description": "The path to a directory containing taxdump files.",
"help_text": "At least nodes.dmp and names.dmp are required. A merged.dmp file is optional."
} }
}, },
"fa_icon": "fas fa-chart-line" "fa_icon": "fas fa-chart-line"