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Sofia Stamouli 2022-10-18 17:48:40 +02:00
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docs/usage.md
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@ -165,9 +165,11 @@ work # Directory containing the nextflow working files
.nextflow_log # Log file from Nextflow
# Other nextflow hidden files, eg. history of pipeline runs and old logs.
```
### Sequencing quality control
nf-core taxprofiler offers [`Falco`](https://github.com/smithlabcode/falco] as an alternative option to [`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
### Preprocessing Steps
nf-core/taxprofiler offers four main preprocessing steps

50
nextflow_schema.json
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@ -10,11 +10,7 @@
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": [
"input",
"outdir",
"databases"
],
"required": ["input", "outdir", "databases"],
"properties": {
"input": {
"type": "string",
@ -84,10 +80,7 @@
"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"
},
@ -140,11 +133,7 @@
"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"
},
@ -178,10 +167,7 @@
"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++"
},
@ -355,15 +341,7 @@
"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`"
@ -382,14 +360,7 @@
"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`"
@ -584,14 +555,7 @@
"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": {