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sofstam 2022-11-29 11:25:52 +01:00
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commit 5254b8d679
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nextflow_schema.json
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@ -10,11 +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", "databases", "outdir"],
"input",
"databases",
"outdir"
],
"properties": { "properties": {
"input": { "input": {
"type": "string", "type": "string",
@ -84,10 +80,7 @@
"shortread_qc_tool": { "shortread_qc_tool": {
"type": "string", "type": "string",
"default": "fastp", "default": "fastp",
"enum": [ "enum": ["fastp", "adapterremoval"],
"fastp",
"adapterremoval"
],
"fa_icon": "fas fa-tools", "fa_icon": "fas fa-tools",
"description": "Specify which tool to use for short-read QC" "description": "Specify which tool to use for short-read QC"
}, },
@ -146,11 +139,7 @@
"shortread_complexityfilter_tool": { "shortread_complexityfilter_tool": {
"type": "string", "type": "string",
"default": "bbduk", "default": "bbduk",
"enum": [ "enum": ["bbduk", "prinseqplusplus", "fastp"],
"bbduk",
"prinseqplusplus",
"fastp"
],
"fa_icon": "fas fa-hammer", "fa_icon": "fas fa-hammer",
"description": "Specify which tool to use for complexity filtering" "description": "Specify which tool to use for complexity filtering"
}, },
@ -184,10 +173,7 @@
"shortread_complexityfilter_prinseqplusplus_mode": { "shortread_complexityfilter_prinseqplusplus_mode": {
"type": "string", "type": "string",
"default": "entropy", "default": "entropy",
"enum": [ "enum": ["entropy", "dust"],
"entropy",
"dust"
],
"fa_icon": "fas fa-check-square", "fa_icon": "fas fa-check-square",
"description": "Specify the complexity filter mode for PRINSEQ++" "description": "Specify the complexity filter mode for PRINSEQ++"
}, },
@ -361,15 +347,7 @@
"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"
],
"fa_icon": "fas fa-file", "fa_icon": "fas fa-file",
"description": "Specify output format from DIAMOND profiling.", "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`" "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`"
@ -388,14 +366,7 @@
"kaiju_taxon_rank": { "kaiju_taxon_rank": {
"type": "string", "type": "string",
"default": "species", "default": "species",
"enum": [ "enum": ["phylum", "class", "order", "family", "genus", "species"],
"phylum",
"class",
"order",
"family",
"genus",
"species"
],
"fa_icon": "fas fa-tag", "fa_icon": "fas fa-tag",
"description": "Specify taxonomic rank to be displayed in Kaiju taxon table", "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`" "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`"
@ -765,23 +736,20 @@
"preprocessing_qc_tool": { "preprocessing_qc_tool": {
"type": "string", "type": "string",
"default": "fastqc", "default": "fastqc",
"enum": [ "enum": ["fastqc", "falco"],
"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.", "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" "description": "Specify the tool used for quality control of raw sequencing reads"
}, },
"save_mgc_counts": { "save_mgc_counts": {
"type": "string", "type": "boolean",
"description": "Save the mgc reads count in mOTUs." "description": "Save the mgc reads count in mOTUs."
}, },
"save_ncbi_id": { "save_ncbi_id": {
"type": "string", "type": "boolean",
"description": "Print NCBI id in mOTUs." "description": "Print NCBI id in mOTUs."
}, },
"save_read_counts": { "save_read_counts": {
"type": "string", "type": "boolean",
"description": "Print result as counts instead of relative abundances in mOTUs." "description": "Print result as counts instead of relative abundances in mOTUs."
} }
} }