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Merge pull request #176 from nf-core/update_motus

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Include NCBI taxid, read counts and mgc arguments in motus
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Sofia Stamouli 2022-12-02 12:18:58 +01:00 committed by GitHub
commit c56c6ea694
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4 changed files with 26 additions and 1 deletions
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7
conf/modules.config
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@ -457,6 +457,13 @@ process {
} }
withName: MOTUS_PROFILE { withName: MOTUS_PROFILE {
ext.args = {
[
params.motus_remove_ncbi_ids ? "" : "-p",
params.motus_use_relative_abundance ? "" : "-c",
params.motus_save_mgc_read_counts ? "-M ${task.ext.prefix}.mgc" : ""
].join(',').replaceAll(','," ")
}
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" } ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [ publishDir = [
path: { "${params.outdir}/motus/${meta.db_name}/" }, path: { "${params.outdir}/motus/${meta.db_name}/" },

3
conf/test_motus.config
View file

@ -44,5 +44,8 @@ params {
run_diamond = false run_diamond = false
run_krakenuniq = false run_krakenuniq = false
run_motus = true run_motus = true
motus_save_mgc_read_counts = false
motus_remove_ncbi_ids = false
motus_use_relative_abundance = false
run_profile_standardisation = true run_profile_standardisation = true
} }

5
nextflow.config
View file

@ -145,7 +145,10 @@ params {
diamond_save_reads = false // this will override default diamond output format so no taxonomic profile is generated! added directly to module in profiling.nf diamond_save_reads = false // this will override default diamond output format so no taxonomic profile is generated! added directly to module in profiling.nf
// mOTUs // mOTUs
run_motus = false run_motus = false
motus_use_relative_abundance = false
motus_remove_ncbi_ids = false
motus_save_mgc_read_counts = false
// krona // krona
run_krona = false run_krona = false

12
nextflow_schema.json
View file

@ -464,6 +464,18 @@
"type": "boolean", "type": "boolean",
"fa_icon": "fas fa-toggle-on", "fa_icon": "fas fa-toggle-on",
"description": "Turn on profiling with mOTUs. Requires database to be present CSV file passed to --databases" "description": "Turn on profiling with mOTUs. Requires database to be present CSV file passed to --databases"
},
"motus_use_relative_abundance": {
"type": "boolean",
"description": "Turn on printing relative abundance instead of counts."
},
"motus_save_mgc_read_counts": {
"type": "boolean",
"description": "Turn on saving the mgc reads count."
},
"motus_remove_ncbi_ids": {
"type": "boolean",
"description": "Turn on removing NCBI taxonomic IDs."
} }
}, },
"fa_icon": "fas fa-align-center" "fa_icon": "fas fa-align-center"