mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-13 07:13:10 +00:00
Update nextflow_schema
This commit is contained in:
parent
afdebaf09a
commit
fa1c132635
1 changed files with 61 additions and 6 deletions
|
@ -10,7 +10,10 @@
|
|||
"type": "object",
|
||||
"fa_icon": "fas fa-terminal",
|
||||
"description": "Define where the pipeline should find input data and save output data.",
|
||||
"required": ["input", "outdir"],
|
||||
"required": [
|
||||
"input",
|
||||
"outdir"
|
||||
],
|
||||
"properties": {
|
||||
"input": {
|
||||
"type": "string",
|
||||
|
@ -173,7 +176,14 @@
|
|||
"description": "Method used to save pipeline results to output directory.",
|
||||
"help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
|
||||
"fa_icon": "fas fa-copy",
|
||||
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
|
||||
"enum": [
|
||||
"symlink",
|
||||
"rellink",
|
||||
"link",
|
||||
"copy",
|
||||
"copyNoFollow",
|
||||
"move"
|
||||
],
|
||||
"hidden": true
|
||||
},
|
||||
"email_on_fail": {
|
||||
|
@ -294,7 +304,10 @@
|
|||
"shortread_clipmerge_tool": {
|
||||
"type": "string",
|
||||
"default": "fastp",
|
||||
"enum": ["fastp", "adapterremoval"]
|
||||
"enum": [
|
||||
"fastp",
|
||||
"adapterremoval"
|
||||
]
|
||||
},
|
||||
"shortread_clipmerge_skipadaptertrim": {
|
||||
"type": "boolean"
|
||||
|
@ -335,7 +348,10 @@
|
|||
"shortread_complexityfilter_prinseqplusplus_mode": {
|
||||
"type": "string",
|
||||
"default": "entropy",
|
||||
"enum": ["entropy", "dust"]
|
||||
"enum": [
|
||||
"entropy",
|
||||
"dust"
|
||||
]
|
||||
},
|
||||
"shortread_complexityfilter_prinseqplusplus_dustscore": {
|
||||
"type": "number",
|
||||
|
@ -388,7 +404,14 @@
|
|||
"kaiju_taxon_name": {
|
||||
"type": "string",
|
||||
"default": "species",
|
||||
"enum": ["phylum", "class", "order", "family", "genus", "species"]
|
||||
"enum": [
|
||||
"phylum",
|
||||
"class",
|
||||
"order",
|
||||
"family",
|
||||
"genus",
|
||||
"species"
|
||||
]
|
||||
},
|
||||
"run_diamond": {
|
||||
"type": "boolean"
|
||||
|
@ -396,7 +419,39 @@
|
|||
"diamond_output_format": {
|
||||
"type": "string",
|
||||
"default": "tsv",
|
||||
"enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"]
|
||||
"enum": [
|
||||
"blast",
|
||||
"xml",
|
||||
"txt",
|
||||
"daa",
|
||||
"sam",
|
||||
"tsv",
|
||||
"paf"
|
||||
]
|
||||
},
|
||||
"longread_hostremoval_index": {
|
||||
"type": "string",
|
||||
"default": null
|
||||
},
|
||||
"save_minimap2_hostremoval_index": {
|
||||
"type": "string",
|
||||
"default": "false",
|
||||
"description": "Flag for publishing minimap2 host removal index"
|
||||
},
|
||||
"save_minimap2_hostremoval_mapped": {
|
||||
"type": "string",
|
||||
"default": "false",
|
||||
"description": "Flag for publishinig bam file with all long reads mapped to a reference"
|
||||
},
|
||||
"save_samtools_unmapped_bam": {
|
||||
"type": "string",
|
||||
"default": "false",
|
||||
"description": "Flag for publishing bam for reads that did not map to the host reference"
|
||||
},
|
||||
"save_minimap2_unmapped_fq": {
|
||||
"type": "string",
|
||||
"default": "false",
|
||||
"description": "Flag for publishing fastq files for reads that did not map to the host reference"
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
Loading…
Reference in a new issue