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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}-${meta.db_name}" } ext.prefix = params.perform_runmerging ? { "${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 = [

2
docs/usage.md
View file

@ -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

43
nextflow_schema.json
View file

@ -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"
]
} }
} }
} }