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Fix conflict
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sofstam
parent
f389029848
commit
12dd836e9c
1 changed files with 778 additions and 748 deletions
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@ -10,7 +10,11 @@
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"type": "object",
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"fa_icon": "fas fa-terminal",
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"description": "Define where the pipeline should find input data and save output data.",
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"required": ["input", "databases", "outdir"],
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"required": [
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"input",
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"databases",
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"outdir"
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],
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"properties": {
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"input": {
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"type": "string",
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@ -80,7 +84,10 @@
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"shortread_qc_tool": {
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"type": "string",
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"default": "fastp",
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"enum": ["fastp", "adapterremoval"],
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"enum": [
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"fastp",
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"adapterremoval"
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],
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"fa_icon": "fas fa-tools",
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"description": "Specify which tool to use for short-read QC"
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},
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@ -139,7 +146,11 @@
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"shortread_complexityfilter_tool": {
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"type": "string",
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"default": "bbduk",
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"enum": ["bbduk", "prinseqplusplus", "fastp"],
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"enum": [
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"bbduk",
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"prinseqplusplus",
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"fastp"
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],
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"fa_icon": "fas fa-hammer",
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"description": "Specify which tool to use for complexity filtering"
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},
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@ -173,7 +184,10 @@
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"shortread_complexityfilter_prinseqplusplus_mode": {
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"type": "string",
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"default": "entropy",
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"enum": ["entropy", "dust"],
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"enum": [
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"entropy",
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"dust"
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],
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"fa_icon": "fas fa-check-square",
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"description": "Specify the complexity filter mode for PRINSEQ++"
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},
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@ -347,7 +361,15 @@
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"diamond_output_format": {
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"type": "string",
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"default": "tsv",
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"enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"],
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"enum": [
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"blast",
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"xml",
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"txt",
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"daa",
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"sam",
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"tsv",
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"paf"
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],
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"fa_icon": "fas fa-file",
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"description": "Specify output format from DIAMOND profiling.",
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"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`"
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@ -366,7 +388,14 @@
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"kaiju_taxon_rank": {
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"type": "string",
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"default": "species",
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"enum": ["phylum", "class", "order", "family", "genus", "species"],
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"enum": [
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"phylum",
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"class",
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"order",
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"family",
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"genus",
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"species"
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],
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"fa_icon": "fas fa-tag",
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"description": "Specify taxonomic rank to be displayed in Kaiju taxon table",
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"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`"
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@ -432,6 +461,18 @@
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"type": "boolean",
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"fa_icon": "fas fa-toggle-on",
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"description": "Turn on profiling with mOTUs. Requires database to be present CSV file passed to --databases"
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},
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"save_mgc_counts": {
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"type": "boolean",
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"description": "Save the mgc reads count for mOTUs."
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},
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"save_read_counts": {
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"type": "boolean",
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"description": "Print mOTUs result as counts instead of relative abundances."
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},
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"save_ncbi_id": {
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"type": "boolean",
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"description": "Print NCBI taxonomic id for mOTUs."
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}
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},
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"fa_icon": "fas fa-align-center"
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@ -607,7 +648,10 @@
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"preprocessing_qc_tool": {
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"type": "string",
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"default": "fastqc",
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"enum": ["fastqc", "falco"],
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"enum": [
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"fastqc",
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"falco"
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],
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"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.",
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"description": "Specify the tool used for quality control of raw sequencing reads"
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},
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@ -738,19 +782,5 @@
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{
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"$ref": "#/definitions/reference_genome_options"
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}
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],
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"properties": {
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"save_mgc_counts": {
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"type": "boolean",
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"description": "Save the mgc reads count for mOTUs."
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},
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"save_ncbi_id": {
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"type": "boolean",
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"description": "Print NCBI taxonomic id for mOTUs."
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},
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"save_read_counts": {
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"type": "boolean",
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"description": "Print mOTUs result as counts instead of relative abundances."
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}
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}
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]
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}
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