mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-13 07:03:10 +00:00
Apply review suggestions
This commit is contained in:
parent
e85c75dcba
commit
933b820c19
4 changed files with 20 additions and 27 deletions
|
@ -448,9 +448,9 @@ process {
|
|||
withName: MOTUS_PROFILE {
|
||||
ext.args = {
|
||||
[
|
||||
params.save_ncbi_id ? "-p" : "",
|
||||
params.save_read_counts ? "-c" : "",
|
||||
params.save_mgc_counts ? "-M ${task.ext.prefix}.mgc" : ""
|
||||
params.motus_ncbi_id ? "-p" : "",
|
||||
params.motus_read_counts ? "-c" : "",
|
||||
params.motus_mgc_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}" }
|
||||
|
|
|
@ -39,8 +39,8 @@ params {
|
|||
run_centrifuge = false
|
||||
run_diamond = false
|
||||
run_motus = true
|
||||
save_mgc_counts = true
|
||||
save_ncbi_id = true
|
||||
save_read_counts = true
|
||||
motus_mgc_counts = true
|
||||
motus_ncbi_id = true
|
||||
motus_read_counts = true
|
||||
run_profile_standardisation = true
|
||||
}
|
||||
|
|
|
@ -140,9 +140,9 @@ params {
|
|||
|
||||
// mOTUs
|
||||
run_motus = false
|
||||
save_mgc_counts = false
|
||||
save_ncbi_id = false
|
||||
save_read_counts = false
|
||||
motus_mgc_counts = false
|
||||
motus_ncbi_id = false
|
||||
motus_read_counts = false
|
||||
|
||||
// krona
|
||||
run_krona = false
|
||||
|
|
|
@ -63,7 +63,10 @@
|
|||
"preprocessing_qc_tool": {
|
||||
"type": "string",
|
||||
"default": "fastqc",
|
||||
"enum": ["fastqc", "falco"],
|
||||
"enum": [
|
||||
"fastqc",
|
||||
"falco"
|
||||
],
|
||||
"help_text": "Falco is designed as a drop-in replacement for FastQC but written in C++ for faster computation. We particularly recommend using falco when using long reads (due to reduced memory constraints), however is also applicable for short reads.",
|
||||
"description": "Specify the tool used for quality control of raw sequencing reads",
|
||||
"fa_icon": "fas fa-tools"
|
||||
|
@ -470,17 +473,17 @@
|
|||
"fa_icon": "fas fa-toggle-on",
|
||||
"description": "Turn on profiling with mOTUs. Requires database to be present CSV file passed to --databases"
|
||||
},
|
||||
"save_mgc_counts": {
|
||||
"motus_mgc_counts": {
|
||||
"type": "boolean",
|
||||
"description": "Save the mgc reads count for mOTUs."
|
||||
"description": "Save the mgc reads count."
|
||||
},
|
||||
"save_read_counts": {
|
||||
"motus_ncbi_id": {
|
||||
"type": "boolean",
|
||||
"description": "Print mOTUs result as counts instead of relative abundances."
|
||||
"description": "Print NCBI id."
|
||||
},
|
||||
"save_ncbi_id": {
|
||||
"motus_read_counts": {
|
||||
"type": "boolean",
|
||||
"description": "Print NCBI taxonomic id for mOTUs."
|
||||
"description": "Print result as counts instead of relative abundances."
|
||||
}
|
||||
},
|
||||
"fa_icon": "fas fa-align-center"
|
||||
|
@ -653,16 +656,6 @@
|
|||
"fa_icon": "fas fa-file-upload",
|
||||
"hidden": true
|
||||
},
|
||||
"preprocessing_qc_tool": {
|
||||
"type": "string",
|
||||
"default": "fastqc",
|
||||
"enum": [
|
||||
"fastqc",
|
||||
"falco"
|
||||
],
|
||||
"help_text": "Falco is designed as a drop-in replacement for FastQC but written in C++ for faster computation. We particularly recommend using falco when using long reads (due to reduced memory constraints), however is also applicable for short reads.",
|
||||
"description": "Specify the tool used for quality control of raw sequencing reads"
|
||||
},
|
||||
"monochrome_logs": {
|
||||
"type": "boolean",
|
||||
"description": "Do not use coloured log outputs.",
|
||||
|
@ -791,4 +784,4 @@
|
|||
"$ref": "#/definitions/reference_genome_options"
|
||||
}
|
||||
]
|
||||
}
|
||||
}
|
||||
|
|
Loading…
Reference in a new issue