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Update schema
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parent
4e93abc7c0
commit
ff1f28f4f0
2 changed files with 37 additions and 5 deletions
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@ -69,8 +69,8 @@ process {
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params.shortread_clipmerge_excludeunmerged ? '' : "--include_unmerged",
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// trimming options
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params.shortread_clipmerge_skiptrim ? "--disable_adapter_trimming" : "",
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params.shortread_adapter1 ? "--adapter_sequence ${params.shortread_adapter1}" : "",
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!{ ${meta.single_end} } && params.shortread_adapter2 ? "--adapter_sequence_r2 ${params.shortread_adapter2}" : !{ ${meta.single_end} } ? "--detect_adapter_for_pe" : ""
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params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
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!{ ${meta.single_end} } && params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : !{ ${meta.single_end} } ? "--detect_adapter_for_pe" : "",
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// filtering options
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"--length_required ${params.shortread_clipmerge_minlength}"
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].join(' ').trim()
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@ -10,7 +10,10 @@
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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": ["input", "outdir"],
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"required": [
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"input",
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"outdir"
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],
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"properties": {
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"input": {
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"type": "string",
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@ -173,7 +176,14 @@
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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": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
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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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"hidden": true
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},
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"email_on_fail": {
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@ -281,6 +291,28 @@
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},
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"run_kraken2": {
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"type": "boolean"
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},
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"shortread_clipmerge_tool": {
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"type": "string",
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"default": "fastp"
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},
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"shortread_clipmerge_skiptrim": {
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"type": "boolean"
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},
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"shortread_clipmerge_mergepairs": {
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"type": "boolean"
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},
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"shortread_clipmerge_adapter1": {
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"type": "string",
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"default": null
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},
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"shortread_clipmerge_adapter2": {
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"type": "string",
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"default": null
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},
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"shortread_clipmerge_minlength": {
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"type": "integer",
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"default": 15
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}
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}
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}
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}
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