mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-22 03:39:55 +00:00
Update nextflow_schema.json
This commit is contained in:
sofstam
parent
49af33f68e
commit
0235ef42ca
1 changed files with 60 additions and 9 deletions
|
|
@ -10,7 +10,11 @@
|
|||
"type": "object",
|
||||
"fa_icon": "fas fa-terminal",
|
||||
"description": "Define where the pipeline should find input data and save output data.",
|
||||
"required": ["input", "databases", "outdir"],
|
||||
"required": [
|
||||
"input",
|
||||
"databases",
|
||||
"outdir"
|
||||
],
|
||||
"properties": {
|
||||
"input": {
|
||||
"type": "string",
|
||||
|
|
@ -80,7 +84,10 @@
|
|||
"shortread_qc_tool": {
|
||||
"type": "string",
|
||||
"default": "fastp",
|
||||
"enum": ["fastp", "adapterremoval"],
|
||||
"enum": [
|
||||
"fastp",
|
||||
"adapterremoval"
|
||||
],
|
||||
"fa_icon": "fas fa-tools",
|
||||
"description": "Specify which tool to use for short-read QC"
|
||||
},
|
||||
|
|
@ -139,7 +146,11 @@
|
|||
"shortread_complexityfilter_tool": {
|
||||
"type": "string",
|
||||
"default": "bbduk",
|
||||
"enum": ["bbduk", "prinseqplusplus", "fastp"],
|
||||
"enum": [
|
||||
"bbduk",
|
||||
"prinseqplusplus",
|
||||
"fastp"
|
||||
],
|
||||
"fa_icon": "fas fa-hammer",
|
||||
"description": "Specify which tool to use for complexity filtering"
|
||||
},
|
||||
|
|
@ -173,7 +184,10 @@
|
|||
"shortread_complexityfilter_prinseqplusplus_mode": {
|
||||
"type": "string",
|
||||
"default": "entropy",
|
||||
"enum": ["entropy", "dust"],
|
||||
"enum": [
|
||||
"entropy",
|
||||
"dust"
|
||||
],
|
||||
"fa_icon": "fas fa-check-square",
|
||||
"description": "Specify the complexity filter mode for PRINSEQ++"
|
||||
},
|
||||
|
|
@ -347,7 +361,15 @@
|
|||
"diamond_output_format": {
|
||||
"type": "string",
|
||||
"default": "tsv",
|
||||
"enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"],
|
||||
"enum": [
|
||||
"blast",
|
||||
"xml",
|
||||
"txt",
|
||||
"daa",
|
||||
"sam",
|
||||
"tsv",
|
||||
"paf"
|
||||
],
|
||||
"fa_icon": "fas fa-file",
|
||||
"description": "Specify output format from DIAMOND profiling.",
|
||||
"help_text": "DIAMOND can produce output in a number of different formats, you can specify here which to produce.\n\nNote that DIAMOND can only produce one format at a time, and depending on which you pick, some downstream steps may not be executed. For example, selecting `daa` or `sam` will mean you will not get a tabular taxonomic profile as with the other tools.\n\nWill be overriden by `--diamond_save_reads.`\n\n> Modifies tool parameter(s):\n> - diamond blastx: `--outfmt`"
|
||||
|
|
@ -366,7 +388,14 @@
|
|||
"kaiju_taxon_rank": {
|
||||
"type": "string",
|
||||
"default": "species",
|
||||
"enum": ["phylum", "class", "order", "family", "genus", "species"],
|
||||
"enum": [
|
||||
"phylum",
|
||||
"class",
|
||||
"order",
|
||||
"family",
|
||||
"genus",
|
||||
"species"
|
||||
],
|
||||
"fa_icon": "fas fa-tag",
|
||||
"description": "Specify taxonomic rank to be displayed in Kaiju taxon table",
|
||||
"help_text": "Specify the taxonomic level(s) to be displayed in the resulting Kaiju taxon table, as generated by the kaiju2table helper tool.\n\nThis can be either a single level (e.g. `species`), or a comma separated list to display the full taxonomic path (e.g. `superkingdom,phylum,class,order,family,genus,species.`).\n\n> Modifies tool parameter(s):\n> - kaiju2table: `-l`"
|
||||
|
|
@ -572,7 +601,14 @@
|
|||
"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": {
|
||||
|
|
@ -729,9 +765,24 @@
|
|||
"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"
|
||||
},
|
||||
"save_mgc_counts": {
|
||||
"type": "string",
|
||||
"description": "Save the mgc reads count in mOTUs."
|
||||
},
|
||||
"save_ncbi_id": {
|
||||
"type": "string",
|
||||
"description": "Print NCBI id in mOTUs."
|
||||
},
|
||||
"save_read_counts": {
|
||||
"type": "string",
|
||||
"description": "Print result as counts instead of relative abundances in mOTUs."
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
Loading…
Reference in a new issue