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James Fellows Yates 2022-07-12 11:41:07 +02:00
parent a0ee82bf43
commit d8c0e9e7fe
1 changed files with 7 additions and 42 deletions
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49
nextflow_schema.json
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@ -10,10 +10,7 @@
"type": "object", "type": "object",
"fa_icon": "fas fa-terminal", "fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.", "description": "Define where the pipeline should find input data and save output data.",
"required": [ "required": ["input", "outdir"],
"input",
"outdir"
],
"properties": { "properties": {
"input": { "input": {
"type": "string", "type": "string",
@ -177,14 +174,7 @@
"description": "Method used to save pipeline results to output directory.", "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.", "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", "fa_icon": "fas fa-copy",
"enum": [ "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
"symlink",
"rellink",
"link",
"copy",
"copyNoFollow",
"move"
],
"hidden": true "hidden": true
}, },
"email_on_fail": { "email_on_fail": {
@ -298,10 +288,7 @@
"shortread_qc_tool": { "shortread_qc_tool": {
"type": "string", "type": "string",
"default": "fastp", "default": "fastp",
"enum": [ "enum": ["fastp", "adapterremoval"]
"fastp",
"adapterremoval"
]
}, },
"shortread_qc_skipadaptertrim": { "shortread_qc_skipadaptertrim": {
"type": "boolean" "type": "boolean"
@ -327,11 +314,7 @@
"shortread_complexityfilter_tool": { "shortread_complexityfilter_tool": {
"type": "string", "type": "string",
"default": "bbduk", "default": "bbduk",
"enum": [ "enum": ["bbduk", "prinseqplusplus", "fastp"]
"bbduk",
"prinseqplusplus",
"fastp"
]
}, },
"shortread_complexityfilter_bbduk_windowsize": { "shortread_complexityfilter_bbduk_windowsize": {
"type": "integer", "type": "integer",
@ -347,10 +330,7 @@
"shortread_complexityfilter_prinseqplusplus_mode": { "shortread_complexityfilter_prinseqplusplus_mode": {
"type": "string", "type": "string",
"default": "entropy", "default": "entropy",
"enum": [ "enum": ["entropy", "dust"]
"entropy",
"dust"
]
}, },
"shortread_complexityfilter_prinseqplusplus_dustscore": { "shortread_complexityfilter_prinseqplusplus_dustscore": {
"type": "number", "type": "number",
@ -406,14 +386,7 @@
"kaiju_taxon_name": { "kaiju_taxon_name": {
"type": "string", "type": "string",
"default": "species", "default": "species",
"enum": [ "enum": ["phylum", "class", "order", "family", "genus", "species"]
"phylum",
"class",
"order",
"family",
"genus",
"species"
]
}, },
"run_diamond": { "run_diamond": {
"type": "boolean" "type": "boolean"
@ -421,15 +394,7 @@
"diamond_output_format": { "diamond_output_format": {
"type": "string", "type": "string",
"default": "tsv", "default": "tsv",
"enum": [ "enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"]
"blast",
"xml",
"txt",
"daa",
"sam",
"tsv",
"paf"
]
}, },
"longread_hostremoval_index": { "longread_hostremoval_index": {
"type": "string", "type": "string",