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Prettier linting and update schema
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3 changed files with 47 additions and 6 deletions
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@ -56,7 +56,7 @@ params {
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// FASTQ preprocessing
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shortread_clipmerge = false
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shortread_excludeunmerged = true
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shortread_excludeunmerged = true
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longread_clip = false
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// MALT
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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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@ -256,5 +266,35 @@
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{
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"$ref": "#/definitions/generic_options"
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}
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]
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}
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],
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"properties": {
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"databases": {
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"type": "string",
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"default": null
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},
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"shortread_clipmerge": {
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"type": "string",
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"default": "false"
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},
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"shortread_excludeunmerged": {
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"type": "string",
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"default": "true"
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},
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"longread_clip": {
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"type": "string",
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"default": "false"
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},
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"run_malt": {
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"type": "string",
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"default": "false"
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},
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"malt_mode": {
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"type": "string",
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"default": "BlastN"
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},
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"run_kraken2": {
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"type": "string",
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"default": "false"
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}
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}
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}
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@ -88,8 +88,9 @@ workflow TAXPROFILER {
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//
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// MODULE: Run FastQC
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//
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ch_input_for_fastqc = INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore ).dump(tag: "input_to_fastq")
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FASTQC (
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INPUT_CHECK.out.fastq.mix( INPUT_CHECK.out.nanopore )
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ch_input_for_fastqc
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)
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ch_versions = ch_versions.mix(FASTQC.out.versions.first())
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