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James Fellows Yates 2022-04-29 22:02:44 +02:00
parent 8126d16dee
commit a4a9b161d8
4 changed files with 11 additions and 42 deletions
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4
conf/modules.config
View file

@ -274,7 +274,7 @@ process {
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
}
withName: KAIJU_KAIJU2TABLE {
withName: KAIJU_KAIJU2TABLE {
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [
@ -284,7 +284,7 @@ process {
]
}
withName: DIAMOND_BLASTX {
withName: DIAMOND_BLASTX {
ext.args = { "${meta.db_params}" }
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
publishDir = [

2
docs/usage.md
View file

@ -129,7 +129,7 @@ Expected (uncompressed) database files for each tool are as follows:
- `nodes.dmp`
- `names.dmp`
- **DIAMOND** output of `diamond makedb`. Note: requires building with taxonomy files
to generate taxonomic profile. See [DIAMOND documentation](https://github.com/bbuchfink/diamond/wiki/3.-Command-line-options#makedb-options). A file named:
to generate taxonomic profile. See [DIAMOND documentation](https://github.com/bbuchfink/diamond/wiki/3.-Command-line-options#makedb-options). A file named:
- `<database_name>.dmnd`
## Running the pipeline

2
modules.json
View file

@ -68,4 +68,4 @@
}
}
}
}
}

45
nextflow_schema.json
View file

@ -10,10 +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"
],
"required": ["input", "outdir"],
"properties": {
"input": {
"type": "string",
@ -176,14 +173,7 @@
"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": {
@ -304,10 +294,7 @@
"shortread_clipmerge_tool": {
"type": "string",
"default": "fastp",
"enum": [
"fastp",
"adapterremoval"
]
"enum": ["fastp", "adapterremoval"]
},
"shortread_clipmerge_skipadaptertrim": {
"type": "boolean"
@ -348,10 +335,7 @@
"shortread_complexityfilter_prinseqplusplus_mode": {
"type": "string",
"default": "entropy",
"enum": [
"entropy",
"dust"
]
"enum": ["entropy", "dust"]
},
"shortread_complexityfilter_prinseqplusplus_dustscore": {
"type": "number",
@ -404,14 +388,7 @@
"kaiju_taxon_name": {
"type": "string",
"default": "species",
"enum": [
"phylum",
"class",
"order",
"family",
"genus",
"species"
]
"enum": ["phylum", "class", "order", "family", "genus", "species"]
},
"run_diamond": {
"type": "boolean"
@ -419,15 +396,7 @@
"diamond_output_format": {
"type": "string",
"default": "tsv",
"enum": [
"blast",
"xml",
"txt",
"daa",
"sam",
"tsv",
"paf"
]
"enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"]
}
}
}
}