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4 changed files with 25 additions and 23 deletions
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@ -448,9 +448,9 @@ process {
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withName: MOTUS_PROFILE {
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ext.args = {
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[
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params.motus_use_ncbi_ids ? "-p" : "",
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params.motus_output_type ? "-c" : "",
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params.motus_save_mgcreadcounts ? "-M ${task.ext.prefix}.mgc" : ""
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params.motus_remove_ncbi_ids ? "" : "-p",
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params.motus_use_relative_abundance ? "" : "-c",
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params.motus_save_mgc_read_counts ? "-M ${task.ext.prefix}.mgc" : ""
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].join(',').replaceAll(','," ")
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}
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ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
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@ -39,8 +39,8 @@ params {
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run_centrifuge = false
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run_diamond = false
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run_motus = true
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motus_save_mgcreadcounts = true
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motus_use_ncbi_ids = true
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motus_output_type = true
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motus_save_mgc_read_counts = true
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motus_remove_ncbi_ids = true
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motus_use_relative_abundance = true
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run_profile_standardisation = true
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}
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@ -140,9 +140,9 @@ params {
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// mOTUs
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run_motus = false
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motus_output_type = false
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motus_use_ncbi_ids = false
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motus_save_mgcreadcounts = false
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motus_use_relative_abundance = false
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motus_remove_ncbi_ids = false
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motus_save_mgc_read_counts = false
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// krona
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run_krona = false
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@ -472,18 +472,6 @@
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"type": "boolean",
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"fa_icon": "fas fa-toggle-on",
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"description": "Turn on profiling with mOTUs. Requires database to be present CSV file passed to --databases"
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},
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"motus_use_ncbi_ids": {
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"type": "boolean",
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"description": "Turn on printing ncbi taxonomic ids."
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},
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"motus_save_mgcreadcounts": {
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"type": "boolean",
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"description": "Turn on saving the mgc reads count to a separate file."
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},
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"motus_output_type": {
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"type": "boolean",
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"description": "Turn on printing result as counts instead of relative abundances."
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}
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},
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"fa_icon": "fas fa-align-center"
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@ -783,5 +771,19 @@
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{
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"$ref": "#/definitions/reference_genome_options"
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}
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]
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],
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"properties": {
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"motus_use_relative_abundance": {
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"type": "string",
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"default": "false"
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},
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"motus_remove_ncbi_ids": {
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"type": "string",
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"default": "false"
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},
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"motus_save_mgc_read_counts": {
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"type": "string",
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"default": "false"
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}
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}
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}
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