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Prettier linting and update schema

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This commit is contained in:
James Fellows Yates 2022-03-24 15:35:09 +01:00
parent 203cd2e7d3
commit cc9368ee52
3 changed files with 47 additions and 6 deletions
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2
nextflow.config
View file

@ -56,7 +56,7 @@ params {
// FASTQ preprocessing // FASTQ preprocessing
shortread_clipmerge = false shortread_clipmerge = false
shortread_excludeunmerged = true shortread_excludeunmerged = true
longread_clip = false longread_clip = false
// MALT // MALT

48
nextflow_schema.json
View file

@ -10,7 +10,10 @@
"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": ["input", "outdir"], "required": [
"input",
"outdir"
],
"properties": { "properties": {
"input": { "input": {
"type": "string", "type": "string",
@ -173,7 +176,14 @@
"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": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], "enum": [
"symlink",
"rellink",
"link",
"copy",
"copyNoFollow",
"move"
],
"hidden": true "hidden": true
}, },
"email_on_fail": { "email_on_fail": {
@ -256,5 +266,35 @@
{ {
"$ref": "#/definitions/generic_options" "$ref": "#/definitions/generic_options"
} }
] ],
} "properties": {
"databases": {
"type": "string",
"default": null
},
"shortread_clipmerge": {
"type": "string",
"default": "false"
},
"shortread_excludeunmerged": {
"type": "string",
"default": "true"
},
"longread_clip": {
"type": "string",
"default": "false"
},
"run_malt": {
"type": "string",
"default": "false"
},
"malt_mode": {
"type": "string",
"default": "BlastN"
},
"run_kraken2": {
"type": "string",
"default": "false"
}
}
}

3
workflows/taxprofiler.nf
View file

@ -88,8 +88,9 @@ workflow TAXPROFILER {
// //
// MODULE: Run FastQC // MODULE: Run FastQC
// //
ch_input_for_fastqc = INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore ).dump(tag: "input_to_fastq")
FASTQC ( FASTQC (
INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore ) ch_input_for_fastqc
) )
ch_versions = ch_versions.mix(FASTQC.out.versions.first()) ch_versions = ch_versions.mix(FASTQC.out.versions.first())