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Update schema

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This commit is contained in:
James Fellows Yates 2022-03-25 15:01:25 +01:00
parent 4e93abc7c0
commit ff1f28f4f0
2 changed files with 37 additions and 5 deletions
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4
conf/modules.config
View file

@ -69,8 +69,8 @@ process {
params.shortread_clipmerge_excludeunmerged ? '' : "--include_unmerged",
// trimming options
params.shortread_clipmerge_skiptrim ? "--disable_adapter_trimming" : "",
params.shortread_adapter1 ? "--adapter_sequence ${params.shortread_adapter1}" : "",
!{ ${meta.single_end} } && params.shortread_adapter2 ? "--adapter_sequence_r2 ${params.shortread_adapter2}" : !{ ${meta.single_end} } ? "--detect_adapter_for_pe" : ""
params.shortread_clipmerge_adapter1 ? "--adapter_sequence ${params.shortread_clipmerge_adapter1}" : "",
!{ ${meta.single_end} } && params.shortread_clipmerge_adapter2 ? "--adapter_sequence_r2 ${params.shortread_clipmerge_adapter2}" : !{ ${meta.single_end} } ? "--detect_adapter_for_pe" : "",
// filtering options
"--length_required ${params.shortread_clipmerge_minlength}"
].join(' ').trim()

38
nextflow_schema.json
View file

@ -10,7 +10,10 @@
"type": "object",
"fa_icon": "fas fa-terminal",
"description": "Define where the pipeline should find input data and save output data.",
"required": ["input", "outdir"],
"required": [
"input",
"outdir"
],
"properties": {
"input": {
"type": "string",
@ -173,7 +176,14 @@
"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.",
"fa_icon": "fas fa-copy",
"enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"],
"enum": [
"symlink",
"rellink",
"link",
"copy",
"copyNoFollow",
"move"
],
"hidden": true
},
"email_on_fail": {
@ -281,6 +291,28 @@
},
"run_kraken2": {
"type": "boolean"
},
"shortread_clipmerge_tool": {
"type": "string",
"default": "fastp"
},
"shortread_clipmerge_skiptrim": {
"type": "boolean"
},
"shortread_clipmerge_mergepairs": {
"type": "boolean"
},
"shortread_clipmerge_adapter1": {
"type": "string",
"default": null
},
"shortread_clipmerge_adapter2": {
"type": "string",
"default": null
},
"shortread_clipmerge_minlength": {
"type": "integer",
"default": 15
}
}
}
}