mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-11 00:13:09 +00:00
Lintin
This commit is contained in:
parent
8126d16dee
commit
a4a9b161d8
4 changed files with 11 additions and 42 deletions
|
@ -274,7 +274,7 @@ process {
|
||||||
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
|
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: KAIJU_KAIJU2TABLE {
|
withName: KAIJU_KAIJU2TABLE {
|
||||||
ext.args = { "${meta.db_params}" }
|
ext.args = { "${meta.db_params}" }
|
||||||
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
|
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
|
||||||
publishDir = [
|
publishDir = [
|
||||||
|
@ -284,7 +284,7 @@ process {
|
||||||
]
|
]
|
||||||
}
|
}
|
||||||
|
|
||||||
withName: DIAMOND_BLASTX {
|
withName: DIAMOND_BLASTX {
|
||||||
ext.args = { "${meta.db_params}" }
|
ext.args = { "${meta.db_params}" }
|
||||||
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
|
ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }
|
||||||
publishDir = [
|
publishDir = [
|
||||||
|
|
|
@ -129,7 +129,7 @@ Expected (uncompressed) database files for each tool are as follows:
|
||||||
- `nodes.dmp`
|
- `nodes.dmp`
|
||||||
- `names.dmp`
|
- `names.dmp`
|
||||||
- **DIAMOND** output of `diamond makedb`. Note: requires building with taxonomy files
|
- **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`
|
- `<database_name>.dmnd`
|
||||||
|
|
||||||
## Running the pipeline
|
## Running the pipeline
|
||||||
|
|
|
@ -10,10 +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", "outdir"],
|
||||||
"input",
|
|
||||||
"outdir"
|
|
||||||
],
|
|
||||||
"properties": {
|
"properties": {
|
||||||
"input": {
|
"input": {
|
||||||
"type": "string",
|
"type": "string",
|
||||||
|
@ -176,14 +173,7 @@
|
||||||
"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": [
|
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
|
||||||
"symlink",
|
|
||||||
"rellink",
|
|
||||||
"link",
|
|
||||||
"copy",
|
|
||||||
"copyNoFollow",
|
|
||||||
"move"
|
|
||||||
],
|
|
||||||
"hidden": true
|
"hidden": true
|
||||||
},
|
},
|
||||||
"email_on_fail": {
|
"email_on_fail": {
|
||||||
|
@ -304,10 +294,7 @@
|
||||||
"shortread_clipmerge_tool": {
|
"shortread_clipmerge_tool": {
|
||||||
"type": "string",
|
"type": "string",
|
||||||
"default": "fastp",
|
"default": "fastp",
|
||||||
"enum": [
|
"enum": ["fastp", "adapterremoval"]
|
||||||
"fastp",
|
|
||||||
"adapterremoval"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"shortread_clipmerge_skipadaptertrim": {
|
"shortread_clipmerge_skipadaptertrim": {
|
||||||
"type": "boolean"
|
"type": "boolean"
|
||||||
|
@ -348,10 +335,7 @@
|
||||||
"shortread_complexityfilter_prinseqplusplus_mode": {
|
"shortread_complexityfilter_prinseqplusplus_mode": {
|
||||||
"type": "string",
|
"type": "string",
|
||||||
"default": "entropy",
|
"default": "entropy",
|
||||||
"enum": [
|
"enum": ["entropy", "dust"]
|
||||||
"entropy",
|
|
||||||
"dust"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"shortread_complexityfilter_prinseqplusplus_dustscore": {
|
"shortread_complexityfilter_prinseqplusplus_dustscore": {
|
||||||
"type": "number",
|
"type": "number",
|
||||||
|
@ -404,14 +388,7 @@
|
||||||
"kaiju_taxon_name": {
|
"kaiju_taxon_name": {
|
||||||
"type": "string",
|
"type": "string",
|
||||||
"default": "species",
|
"default": "species",
|
||||||
"enum": [
|
"enum": ["phylum", "class", "order", "family", "genus", "species"]
|
||||||
"phylum",
|
|
||||||
"class",
|
|
||||||
"order",
|
|
||||||
"family",
|
|
||||||
"genus",
|
|
||||||
"species"
|
|
||||||
]
|
|
||||||
},
|
},
|
||||||
"run_diamond": {
|
"run_diamond": {
|
||||||
"type": "boolean"
|
"type": "boolean"
|
||||||
|
@ -419,15 +396,7 @@
|
||||||
"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"
|
|
||||||
]
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
}
|
}
|
Loading…
Reference in a new issue