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Linting
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2 changed files with 14 additions and 45 deletions
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@ -55,7 +55,7 @@ process {
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params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
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// filtering options
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"--length_required ${params.shortread_clipmerge_minlength}",
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params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
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params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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@ -76,7 +76,7 @@ process {
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params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : "--detect_adapter_for_pe",
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// filtering options
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"--length_required ${params.shortread_clipmerge_minlength}",
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params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
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params.perform_shortread_complexityfilter && params.shortread_complexityfilter_tool == 'fastp' ? "--low_complexity_filter --complexity_threshold ${params.shortread_complexityfilter_fastp_threshold}" : ''
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].join(' ').trim()
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ext.prefix = { "${meta.id}_${meta.run_accession}" }
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publishDir = [
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@ -10,10 +10,7 @@
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"type": "object",
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"fa_icon": "fas fa-terminal",
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"description": "Define where the pipeline should find input data and save output data.",
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"required": [
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"input",
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"outdir"
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],
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"required": ["input", "outdir"],
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"properties": {
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"input": {
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"type": "string",
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@ -176,14 +173,7 @@
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"description": "Method used to save pipeline results to output directory.",
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"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.",
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"fa_icon": "fas fa-copy",
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"enum": [
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"symlink",
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"rellink",
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"link",
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"copy",
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"copyNoFollow",
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"move"
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],
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"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
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"hidden": true
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},
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"email_on_fail": {
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@ -304,10 +294,7 @@
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"shortread_clipmerge_tool": {
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"type": "string",
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"default": "fastp",
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"enum": [
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"fastp",
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"adapterremoval"
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]
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"enum": ["fastp", "adapterremoval"]
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},
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"shortread_clipmerge_skipadaptertrim": {
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"type": "boolean"
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@ -333,11 +320,7 @@
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"shortread_complexityfilter_tool": {
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"type": "string",
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"default": "bbduk",
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"enum": [
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"bbduk",
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"prinseqplusplus",
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"fastp"
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]
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"enum": ["bbduk", "prinseqplusplus", "fastp"]
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},
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"shortread_complexityfilter_bbduk_windowsize": {
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"type": "integer",
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@ -353,10 +336,7 @@
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"shortread_complexityfilter_prinseqplusplus_mode": {
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"type": "string",
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"default": "entropy",
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"enum": [
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"entropy",
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"dust"
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]
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"enum": ["entropy", "dust"]
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},
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"shortread_complexityfilter_prinseqplusplus_dustscore": {
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"type": "number",
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@ -412,14 +392,7 @@
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"kaiju_taxon_name": {
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"type": "string",
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"default": "species",
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"enum": [
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"phylum",
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"class",
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"order",
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"family",
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"genus",
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"species"
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]
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"enum": ["phylum", "class", "order", "family", "genus", "species"]
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},
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"run_diamond": {
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"type": "boolean"
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@ -427,19 +400,15 @@
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"diamond_output_format": {
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"type": "string",
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"default": "tsv",
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"enum": [
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"blast",
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"xml",
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"txt",
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"daa",
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"sam",
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"tsv",
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"paf"
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]
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"enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"]
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},
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"longread_hostremoval_index": {
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"type": "string",
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"default": "None"
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},
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"shortread_complexityfilter_fastp_threshold": {
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"type": "integer",
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"default": 30
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}
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}
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}
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}
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