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sofstam 2022-12-01 13:42:21 +01:00
parent 1965ade961
commit 38a818fd17
4 changed files with 25 additions and 23 deletions
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6
conf/modules.config
View file

@ -448,9 +448,9 @@ process {
withName: MOTUS_PROFILE { withName: MOTUS_PROFILE {
ext.args = { ext.args = {
[ [
params.motus_use_ncbi_ids ? "-p" : "", params.motus_remove_ncbi_ids ? "" : "-p",
params.motus_output_type ? "-c" : "", params.motus_use_relative_abundance ? "" : "-c",
params.motus_save_mgcreadcounts ? "-M ${task.ext.prefix}.mgc" : "" params.motus_save_mgc_read_counts ? "-M ${task.ext.prefix}.mgc" : ""
].join(',').replaceAll(','," ") ].join(',').replaceAll(','," ")
} }
ext.prefix = params.perform_runmerging ? { "${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}" }

6
conf/test_motus.config
View file

@ -39,8 +39,8 @@ params {
run_centrifuge = false run_centrifuge = false
run_diamond = false run_diamond = false
run_motus = true run_motus = true
motus_save_mgcreadcounts = true motus_save_mgc_read_counts = true
motus_use_ncbi_ids = true motus_remove_ncbi_ids = true
motus_output_type = true motus_use_relative_abundance = true
run_profile_standardisation = true run_profile_standardisation = true
} }

8
nextflow.config
View file

@ -139,10 +139,10 @@ 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_output_type = false motus_use_relative_abundance = false
motus_use_ncbi_ids = false motus_remove_ncbi_ids = false
motus_save_mgcreadcounts = false motus_save_mgc_read_counts = false
// krona // krona
run_krona = false run_krona = false

28
nextflow_schema.json
View file

@ -472,18 +472,6 @@
"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_ncbi_ids": {
"type": "boolean",
"description": "Turn on printing ncbi taxonomic ids."
},
"motus_save_mgcreadcounts": {
"type": "boolean",
"description": "Turn on saving the mgc reads count to a separate file."
},
"motus_output_type": {
"type": "boolean",
"description": "Turn on printing result as counts instead of relative abundances."
} }
}, },
"fa_icon": "fas fa-align-center" "fa_icon": "fas fa-align-center"
@ -783,5 +771,19 @@
{ {
"$ref": "#/definitions/reference_genome_options" "$ref": "#/definitions/reference_genome_options"
} }
] ],
"properties": {
"motus_use_relative_abundance": {
"type": "string",
"default": "false"
},
"motus_remove_ncbi_ids": {
"type": "string",
"default": "false"
},
"motus_save_mgc_read_counts": {
"type": "string",
"default": "false"
}
}
} }