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Update nextflow_schema

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ljmesi 2022-05-03 11:03:25 +02:00
parent afdebaf09a
commit fa1c132635
1 changed files with 61 additions and 6 deletions
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67
nextflow_schema.json
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@ -10,7 +10,10 @@
"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": ["input", "outdir"], "required": [
"input",
"outdir"
],
"properties": { "properties": {
"input": { "input": {
"type": "string", "type": "string",
@ -173,7 +176,14 @@
"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": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], "enum": [
"symlink",
"rellink",
"link",
"copy",
"copyNoFollow",
"move"
],
"hidden": true "hidden": true
}, },
"email_on_fail": { "email_on_fail": {
@ -294,7 +304,10 @@
"shortread_clipmerge_tool": { "shortread_clipmerge_tool": {
"type": "string", "type": "string",
"default": "fastp", "default": "fastp",
"enum": ["fastp", "adapterremoval"] "enum": [
"fastp",
"adapterremoval"
]
}, },
"shortread_clipmerge_skipadaptertrim": { "shortread_clipmerge_skipadaptertrim": {
"type": "boolean" "type": "boolean"
@ -335,7 +348,10 @@
"shortread_complexityfilter_prinseqplusplus_mode": { "shortread_complexityfilter_prinseqplusplus_mode": {
"type": "string", "type": "string",
"default": "entropy", "default": "entropy",
"enum": ["entropy", "dust"] "enum": [
"entropy",
"dust"
]
}, },
"shortread_complexityfilter_prinseqplusplus_dustscore": { "shortread_complexityfilter_prinseqplusplus_dustscore": {
"type": "number", "type": "number",
@ -388,7 +404,14 @@
"kaiju_taxon_name": { "kaiju_taxon_name": {
"type": "string", "type": "string",
"default": "species", "default": "species",
"enum": ["phylum", "class", "order", "family", "genus", "species"] "enum": [
"phylum",
"class",
"order",
"family",
"genus",
"species"
]
}, },
"run_diamond": { "run_diamond": {
"type": "boolean" "type": "boolean"
@ -396,7 +419,39 @@
"diamond_output_format": { "diamond_output_format": {
"type": "string", "type": "string",
"default": "tsv", "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"
} }
} }
} }