From d6d51e0e4388da1693071847563f869990309eb3 Mon Sep 17 00:00:00 2001 From: James Fellows Yates Date: Wed, 24 Aug 2022 15:23:51 +0200 Subject: [PATCH] Start work on reordering json schema parameters --- nextflow_schema.json | 508 ++++++++++++++++++++++++++----------------- 1 file changed, 309 insertions(+), 199 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index b4cb837..70cee15 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -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", @@ -22,6 +25,12 @@ "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).", "fa_icon": "fas fa-file-csv" }, + "databases": { + "type": "string", + "mimetype": "text/csv", + "format": "file-path", + "default": "None" + }, "outdir": { "type": "string", "format": "directory-path", @@ -174,7 +183,14 @@ "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": { @@ -239,6 +255,275 @@ "fa_icon": "fas fa-bacon" } } + }, + "preprocessing_short_read_qc": { + "title": "Preprocessing - Short Read QC", + "type": "object", + "description": "", + "default": "", + "properties": { + "perform_shortread_qc": { + "type": "boolean" + }, + "shortread_qc_tool": { + "type": "string", + "default": "fastp", + "enum": [ + "fastp", + "adapterremoval" + ] + }, + "shortread_qc_skipadaptertrim": { + "type": "boolean" + }, + "shortread_qc_adapter1": { + "type": "string", + "default": "None" + }, + "shortread_qc_adapter2": { + "type": "string", + "default": "None" + }, + "shortread_qc_mergepairs": { + "type": "boolean" + }, + "shortread_qc_excludeunmerged": { + "type": "boolean" + }, + "shortread_qc_minlength": { + "type": "integer", + "default": 15 + }, + "perform_shortread_complexityfilter": { + "type": "boolean" + }, + "shortread_complexityfilter_tool": { + "type": "string", + "default": "bbduk", + "enum": [ + "bbduk", + "prinseqplusplus", + "fastp" + ] + }, + "shortread_complexityfilter_entropy": { + "type": "number", + "default": 0.3 + }, + "shortread_complexityfilter_bbduk_windowsize": { + "type": "integer", + "default": 50 + }, + "shortread_complexityfilter_bbduk_mask": { + "type": "boolean" + }, + "shortread_complexityfilter_fastp_threshold": { + "type": "integer", + "default": 30 + }, + "shortread_complexityfilter_prinseqplusplus_mode": { + "type": "string", + "default": "entropy", + "enum": [ + "entropy", + "dust" + ] + }, + "shortread_complexityfilter_prinseqplusplus_dustscore": { + "type": "number", + "default": 0.5 + }, + "save_complexityfiltered_reads": { + "type": "boolean" + } + } + }, + "profiling": { + "title": "Profiling", + "type": "object", + "description": "", + "default": "", + "properties": { + "run_malt": { + "type": "boolean" + }, + "run_diamond": { + "type": "boolean" + }, + "malt_mode": { + "type": "string", + "default": "BlastN" + }, + "kaiju_taxon_name": { + "type": "string", + "default": "species", + "enum": [ + "phylum", + "class", + "order", + "family", + "genus", + "species" + ] + }, + "run_centrifuge": { + "type": "boolean" + }, + "diamond_output_format": { + "type": "string", + "default": "tsv", + "enum": [ + "blast", + "xml", + "txt", + "daa", + "sam", + "tsv", + "paf" + ] + }, + "malt_generate_megansummary": { + "type": "boolean" + }, + "run_metaphlan3": { + "type": "boolean", + "description": "Enable MetaPhlAn for taxonomic profiling" + }, + "centrifuge_save_reads": { + "type": "boolean" + }, + "run_kaiju": { + "type": "boolean" + }, + "kraken2_save_reads": { + "type": "boolean" + }, + "diamond_save_reads": { + "type": "boolean" + }, + "malt_save_reads": { + "type": "boolean" + }, + "run_motus": { + "type": "boolean" + }, + "kraken2_save_readclassification": { + "type": "boolean" + }, + "run_kraken2": { + "type": "boolean" + } + } + }, + "preprocessing_general_qc": { + "title": "Preprocessing - General QC", + "type": "object", + "description": "", + "default": "", + "properties": { + "save_preprocessed_reads": { + "type": "boolean" + } + } + }, + "preprocessing_long_read_qc": { + "title": "Preprocessing - Long Read QC", + "type": "object", + "description": "", + "default": "", + "properties": { + "perform_longread_qc": { + "type": "boolean" + }, + "longread_qc_run_clip": { + "type": "boolean" + }, + "longread_qc_run_filter": { + "type": "boolean" + }, + "longread_qc_keep_percent": { + "type": "integer", + "default": 90 + }, + "longread_qc_target_bases": { + "type": "integer", + "default": 500000000 + }, + "longread_qc_minlength": { + "type": "integer", + "default": 1000 + }, + "longread_hostremoval_index": { + "type": "string", + "default": "None" + } + } + }, + "preprocessing_host_removal": { + "title": "Preprocessing - Host Removal", + "type": "object", + "description": "", + "default": "", + "properties": { + "perform_shortread_hostremoval": { + "type": "boolean" + }, + "hostremoval_reference": { + "type": "string", + "default": "None" + }, + "perform_longread_hostremoval": { + "type": "boolean" + }, + "save_hostremoval_mapped": { + "type": "boolean" + }, + "save_hostremoval_index": { + "type": "boolean" + }, + "save_hostremoval_unmapped": { + "type": "boolean" + }, + "shortread_hostremoval_index": { + "type": "string", + "default": "None" + } + } + }, + "preprocessing_run_merging": { + "title": "Preprocessing - Run Merging", + "type": "object", + "description": "", + "default": "", + "properties": { + "perform_runmerging": { + "type": "boolean" + }, + "save_runmerged_reads": { + "type": "boolean" + } + } + }, + "postprocessing_and_visualisation": { + "title": "Postprocessing and Visualisation", + "type": "object", + "description": "", + "default": "", + "properties": { + "run_profile_standardisation": { + "type": "boolean" + }, + "krona_taxonomy_directory": { + "type": "string", + "default": "None" + }, + "run_krona": { + "type": "boolean" + }, + "generate_biom_output": { + "type": "boolean" + } + } } }, "allOf": [ @@ -256,202 +541,27 @@ }, { "$ref": "#/definitions/generic_options" + }, + { + "$ref": "#/definitions/preprocessing_short_read_qc" + }, + { + "$ref": "#/definitions/profiling" + }, + { + "$ref": "#/definitions/preprocessing_general_qc" + }, + { + "$ref": "#/definitions/preprocessing_long_read_qc" + }, + { + "$ref": "#/definitions/preprocessing_host_removal" + }, + { + "$ref": "#/definitions/preprocessing_run_merging" + }, + { + "$ref": "#/definitions/postprocessing_and_visualisation" } - ], - "properties": { - "databases": { - "type": "string", - "mimetype": "text/csv", - "format": "file-path", - "default": "None" - }, - "shortread_qc_excludeunmerged": { - "type": "boolean" - }, - "run_malt": { - "type": "boolean" - }, - "malt_mode": { - "type": "string", - "default": "BlastN" - }, - "run_kraken2": { - "type": "boolean" - }, - "run_centrifuge": { - "type": "boolean" - }, - "run_metaphlan3": { - "type": "boolean", - "description": "Enable MetaPhlAn for taxonomic profiling" - }, - "shortread_qc_tool": { - "type": "string", - "default": "fastp", - "enum": ["fastp", "adapterremoval"] - }, - "shortread_qc_skipadaptertrim": { - "type": "boolean" - }, - "shortread_qc_mergepairs": { - "type": "boolean" - }, - "shortread_qc_adapter1": { - "type": "string", - "default": "None" - }, - "shortread_qc_adapter2": { - "type": "string", - "default": "None" - }, - "shortread_qc_minlength": { - "type": "integer", - "default": 15 - }, - "save_preprocessed_reads": { - "type": "boolean" - }, - "shortread_complexityfilter_tool": { - "type": "string", - "default": "bbduk", - "enum": ["bbduk", "prinseqplusplus", "fastp"] - }, - "shortread_complexityfilter_bbduk_windowsize": { - "type": "integer", - "default": 50 - }, - "shortread_complexityfilter_bbduk_mask": { - "type": "boolean" - }, - "shortread_complexityfilter_entropy": { - "type": "number", - "default": 0.3 - }, - "shortread_complexityfilter_prinseqplusplus_mode": { - "type": "string", - "default": "entropy", - "enum": ["entropy", "dust"] - }, - "shortread_complexityfilter_prinseqplusplus_dustscore": { - "type": "number", - "default": 0.5 - }, - "save_complexityfiltered_reads": { - "type": "boolean" - }, - "save_runmerged_reads": { - "type": "boolean" - }, - "perform_shortread_qc": { - "type": "boolean" - }, - "perform_longread_qc": { - "type": "boolean" - }, - "perform_shortread_complexityfilter": { - "type": "boolean" - }, - "perform_runmerging": { - "type": "boolean" - }, - "perform_shortread_hostremoval": { - "type": "boolean" - }, - "perform_longread_hostremoval": { - "type": "boolean" - }, - "hostremoval_reference": { - "type": "string", - "default": "None" - }, - "shortread_hostremoval_index": { - "type": "string", - "default": "None" - }, - "save_hostremoval_index": { - "type": "boolean" - }, - "save_hostremoval_mapped": { - "type": "boolean" - }, - "save_hostremoval_unmapped": { - "type": "boolean" - }, - "run_kaiju": { - "type": "boolean" - }, - "malt_generate_megansummary": { - "type": "boolean" - }, - "kaiju_taxon_name": { - "type": "string", - "default": "species", - "enum": ["phylum", "class", "order", "family", "genus", "species"] - }, - "run_diamond": { - "type": "boolean" - }, - "diamond_output_format": { - "type": "string", - "default": "tsv", - "enum": ["blast", "xml", "txt", "daa", "sam", "tsv", "paf"] - }, - "longread_hostremoval_index": { - "type": "string", - "default": "None" - }, - "shortread_complexityfilter_fastp_threshold": { - "type": "integer", - "default": 30 - }, - "longread_qc_run_clip": { - "type": "boolean" - }, - "longread_qc_run_filter": { - "type": "boolean" - }, - "longread_qc_minlength": { - "type": "integer", - "default": 1000 - }, - "longread_qc_keep_percent": { - "type": "integer", - "default": 90 - }, - "longread_qc_target_bases": { - "type": "integer", - "default": 500000000 - }, - "run_motus": { - "type": "boolean" - }, - "malt_save_reads": { - "type": "boolean" - }, - "kraken2_save_reads": { - "type": "boolean" - }, - "kraken2_save_readclassification": { - "type": "boolean" - }, - "centrifuge_save_reads": { - "type": "boolean" - }, - "diamond_save_reads": { - "type": "boolean" - }, - "run_krona": { - "type": "boolean" - }, - "krona_taxonomy_directory": { - "type": "string", - "default": "None" - }, - "run_profile_standardisation": { - "type": "boolean" - }, - "generate_biom_output": { - "type": "boolean" - } - } + ] }