mirror of
https://github.com/MillironX/taxprofiler.git
synced 2024-11-10 22:13:08 +00:00
Start work on reordering json schema parameters
This commit is contained in:
James Fellows Yates
parent
1821496a49
commit
d6d51e0e43
1 changed files with 309 additions and 199 deletions
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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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@ -22,6 +25,12 @@
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"help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/taxprofiler/usage#samplesheet-input).",
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"fa_icon": "fas fa-file-csv"
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},
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"databases": {
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"type": "string",
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"mimetype": "text/csv",
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"format": "file-path",
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"default": "None"
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},
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"outdir": {
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"type": "string",
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"format": "directory-path",
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@ -174,7 +183,14 @@
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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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@ -239,6 +255,275 @@
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"fa_icon": "fas fa-bacon"
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}
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}
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},
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"preprocessing_short_read_qc": {
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"title": "Preprocessing - Short Read QC",
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"type": "object",
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"description": "",
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"default": "",
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"properties": {
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"perform_shortread_qc": {
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"type": "boolean"
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},
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"shortread_qc_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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},
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"shortread_qc_skipadaptertrim": {
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"type": "boolean"
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},
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"shortread_qc_adapter1": {
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"type": "string",
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"default": "None"
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},
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"shortread_qc_adapter2": {
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"type": "string",
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"default": "None"
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},
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"shortread_qc_mergepairs": {
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"type": "boolean"
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},
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"shortread_qc_excludeunmerged": {
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"type": "boolean"
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},
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"shortread_qc_minlength": {
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"type": "integer",
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"default": 15
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},
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"perform_shortread_complexityfilter": {
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"type": "boolean"
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},
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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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},
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"shortread_complexityfilter_entropy": {
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"type": "number",
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"default": 0.3
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},
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"shortread_complexityfilter_bbduk_windowsize": {
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"type": "integer",
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"default": 50
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},
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"shortread_complexityfilter_bbduk_mask": {
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"type": "boolean"
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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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"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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},
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"shortread_complexityfilter_prinseqplusplus_dustscore": {
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"type": "number",
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"default": 0.5
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},
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"save_complexityfiltered_reads": {
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"type": "boolean"
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}
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}
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},
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"profiling": {
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"title": "Profiling",
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"type": "object",
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"description": "",
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"default": "",
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"properties": {
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"run_malt": {
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"type": "boolean"
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},
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"run_diamond": {
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"type": "boolean"
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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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"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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},
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"run_centrifuge": {
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"type": "boolean"
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},
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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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},
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"malt_generate_megansummary": {
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"type": "boolean"
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},
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"run_metaphlan3": {
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"type": "boolean",
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"description": "Enable MetaPhlAn for taxonomic profiling"
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},
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"centrifuge_save_reads": {
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"type": "boolean"
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},
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"run_kaiju": {
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"type": "boolean"
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},
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"kraken2_save_reads": {
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"type": "boolean"
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},
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"diamond_save_reads": {
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"type": "boolean"
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},
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"malt_save_reads": {
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"type": "boolean"
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},
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"run_motus": {
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"type": "boolean"
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},
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"kraken2_save_readclassification": {
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"type": "boolean"
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},
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"run_kraken2": {
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"type": "boolean"
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}
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}
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},
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"preprocessing_general_qc": {
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"title": "Preprocessing - General QC",
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"type": "object",
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"description": "",
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"default": "",
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"properties": {
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"save_preprocessed_reads": {
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"type": "boolean"
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}
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}
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},
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"preprocessing_long_read_qc": {
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"title": "Preprocessing - Long Read QC",
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"type": "object",
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"description": "",
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"default": "",
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"properties": {
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"perform_longread_qc": {
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"type": "boolean"
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},
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"longread_qc_run_clip": {
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"type": "boolean"
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},
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"longread_qc_run_filter": {
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"type": "boolean"
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},
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"longread_qc_keep_percent": {
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"type": "integer",
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"default": 90
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},
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"longread_qc_target_bases": {
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"type": "integer",
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"default": 500000000
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},
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"longread_qc_minlength": {
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"type": "integer",
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"default": 1000
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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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}
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},
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"preprocessing_host_removal": {
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"title": "Preprocessing - Host Removal",
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"type": "object",
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"description": "",
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"default": "",
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"properties": {
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"perform_shortread_hostremoval": {
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"type": "boolean"
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},
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"hostremoval_reference": {
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"type": "string",
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"default": "None"
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},
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"perform_longread_hostremoval": {
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"type": "boolean"
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},
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"save_hostremoval_mapped": {
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"type": "boolean"
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},
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"save_hostremoval_index": {
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"type": "boolean"
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},
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"save_hostremoval_unmapped": {
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"type": "boolean"
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},
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"shortread_hostremoval_index": {
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"type": "string",
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"default": "None"
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}
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}
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},
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"preprocessing_run_merging": {
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"title": "Preprocessing - Run Merging",
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"type": "object",
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"description": "",
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"default": "",
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"properties": {
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"perform_runmerging": {
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"type": "boolean"
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},
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"save_runmerged_reads": {
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"type": "boolean"
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}
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}
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},
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"postprocessing_and_visualisation": {
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"title": "Postprocessing and Visualisation",
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"type": "object",
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"description": "",
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"default": "",
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"properties": {
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"run_profile_standardisation": {
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"type": "boolean"
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},
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"krona_taxonomy_directory": {
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"type": "string",
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"default": "None"
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},
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"run_krona": {
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"type": "boolean"
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},
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"generate_biom_output": {
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"type": "boolean"
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}
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}
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}
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},
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"allOf": [
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@ -256,202 +541,27 @@
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},
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{
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"$ref": "#/definitions/generic_options"
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},
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{
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"$ref": "#/definitions/preprocessing_short_read_qc"
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},
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{
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"$ref": "#/definitions/profiling"
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},
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{
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"$ref": "#/definitions/preprocessing_general_qc"
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},
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{
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"$ref": "#/definitions/preprocessing_long_read_qc"
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},
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{
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"$ref": "#/definitions/preprocessing_host_removal"
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},
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{
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"$ref": "#/definitions/preprocessing_run_merging"
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},
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{
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"$ref": "#/definitions/postprocessing_and_visualisation"
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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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"mimetype": "text/csv",
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"format": "file-path",
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"default": "None"
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},
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"shortread_qc_excludeunmerged": {
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"type": "boolean"
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},
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"run_malt": {
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"type": "boolean"
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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": "boolean"
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},
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"run_centrifuge": {
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"type": "boolean"
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},
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"run_metaphlan3": {
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"type": "boolean",
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"description": "Enable MetaPhlAn for taxonomic profiling"
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},
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"shortread_qc_tool": {
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"type": "string",
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"default": "fastp",
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"enum": ["fastp", "adapterremoval"]
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},
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"shortread_qc_skipadaptertrim": {
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"type": "boolean"
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},
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"shortread_qc_mergepairs": {
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"type": "boolean"
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},
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"shortread_qc_adapter1": {
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"type": "string",
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"default": "None"
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},
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"shortread_qc_adapter2": {
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"type": "string",
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"default": "None"
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},
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"shortread_qc_minlength": {
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"type": "integer",
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"default": 15
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},
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"save_preprocessed_reads": {
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"type": "boolean"
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},
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"shortread_complexityfilter_tool": {
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"type": "string",
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"default": "bbduk",
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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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"default": 50
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},
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"shortread_complexityfilter_bbduk_mask": {
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"type": "boolean"
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},
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"shortread_complexityfilter_entropy": {
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"type": "number",
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"default": 0.3
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},
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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": ["entropy", "dust"]
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},
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"shortread_complexityfilter_prinseqplusplus_dustscore": {
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"type": "number",
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"default": 0.5
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},
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"save_complexityfiltered_reads": {
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"type": "boolean"
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},
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"save_runmerged_reads": {
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"type": "boolean"
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},
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"perform_shortread_qc": {
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"type": "boolean"
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},
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"perform_longread_qc": {
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"type": "boolean"
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},
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"perform_shortread_complexityfilter": {
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"type": "boolean"
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},
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"perform_runmerging": {
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"type": "boolean"
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},
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"perform_shortread_hostremoval": {
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"type": "boolean"
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},
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"perform_longread_hostremoval": {
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"type": "boolean"
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},
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"hostremoval_reference": {
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"type": "string",
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"default": "None"
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},
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"shortread_hostremoval_index": {
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"type": "string",
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"default": "None"
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},
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"save_hostremoval_index": {
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"type": "boolean"
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},
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"save_hostremoval_mapped": {
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"type": "boolean"
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},
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"save_hostremoval_unmapped": {
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"type": "boolean"
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||||
},
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"run_kaiju": {
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"type": "boolean"
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||||
},
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||||
"malt_generate_megansummary": {
|
||||
"type": "boolean"
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||||
},
|
||||
"kaiju_taxon_name": {
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"type": "string",
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||||
"default": "species",
|
||||
"enum": ["phylum", "class", "order", "family", "genus", "species"]
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||||
},
|
||||
"run_diamond": {
|
||||
"type": "boolean"
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||||
},
|
||||
"diamond_output_format": {
|
||||
"type": "string",
|
||||
"default": "tsv",
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||||
"enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"]
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||||
},
|
||||
"longread_hostremoval_index": {
|
||||
"type": "string",
|
||||
"default": "None"
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||||
},
|
||||
"shortread_complexityfilter_fastp_threshold": {
|
||||
"type": "integer",
|
||||
"default": 30
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||||
},
|
||||
"longread_qc_run_clip": {
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||||
"type": "boolean"
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||||
},
|
||||
"longread_qc_run_filter": {
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||||
"type": "boolean"
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||||
},
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||||
"longread_qc_minlength": {
|
||||
"type": "integer",
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||||
"default": 1000
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||||
},
|
||||
"longread_qc_keep_percent": {
|
||||
"type": "integer",
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||||
"default": 90
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||||
},
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||||
"longread_qc_target_bases": {
|
||||
"type": "integer",
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||||
"default": 500000000
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},
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"run_motus": {
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"type": "boolean"
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},
|
||||
"malt_save_reads": {
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"type": "boolean"
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||||
},
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||||
"kraken2_save_reads": {
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||||
"type": "boolean"
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||||
},
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||||
"kraken2_save_readclassification": {
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"type": "boolean"
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||||
},
|
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"centrifuge_save_reads": {
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"type": "boolean"
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||||
},
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||||
"diamond_save_reads": {
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"type": "boolean"
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||||
},
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"run_krona": {
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"type": "boolean"
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||||
},
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||||
"krona_taxonomy_directory": {
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"type": "string",
|
||||
"default": "None"
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||||
},
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||||
"run_profile_standardisation": {
|
||||
"type": "boolean"
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||||
},
|
||||
"generate_biom_output": {
|
||||
"type": "boolean"
|
||||
}
|
||||
}
|
||||
]
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in a new issue