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James Fellows Yates 2022-05-07 06:12:24 +02:00
parent 47a5ae0cff
commit 0f651873dd
2 changed files with 14 additions and 45 deletions
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4
conf/modules.config
View file

@ -55,7 +55,7 @@ process {
params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "", params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
// filtering options // filtering options
"--length_required ${params.shortread_clipmerge_minlength}", "--length_required ${params.shortread_clipmerge_minlength}",
params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : '' params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
].join(' ').trim() ].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [ publishDir = [
@ -76,7 +76,7 @@ process {
params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : "--detect_adapter_for_pe", params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : "--detect_adapter_for_pe",
// filtering options // filtering options
"--length_required ${params.shortread_clipmerge_minlength}", "--length_required ${params.shortread_clipmerge_minlength}",
params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : '' params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
].join(' ').trim() ].join(' ').trim()
ext.prefix = { "${meta.id}_${meta.run_accession}" } ext.prefix = { "${meta.id}_${meta.run_accession}" }
publishDir = [ publishDir = [

55
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"
@ -333,11 +320,7 @@
"shortread_complexityfilter_tool": { "shortread_complexityfilter_tool": {
"type": "string", "type": "string",
"default": "bbduk", "default": "bbduk",
"enum": [ "enum": ["bbduk", "prinseqplusplus", "fastp"]
"bbduk",
"prinseqplusplus",
"fastp"
]
}, },
"shortread_complexityfilter_bbduk_windowsize": { "shortread_complexityfilter_bbduk_windowsize": {
"type": "integer", "type": "integer",
@ -353,10 +336,7 @@
"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",
@ -412,14 +392,7 @@
"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"
@ -427,19 +400,15 @@
"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"
]
}, },
"longread_hostremoval_index": { "longread_hostremoval_index": {
"type": "string", "type": "string",
"default": "None" "default": "None"
},
"shortread_complexityfilter_fastp_threshold": {
"type": "integer",
"default": 30
} }
} }
} }