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Add mime-type and other fields to main parameter schema
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@drpatelh
drpatelh committed May 13, 2021
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34 changes: 34 additions & 0 deletions nextflow_schema.json
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"properties": {
"input": {
"type": "string",
"format": "file-path",
"mimetype": "text/csv",
"pattern": "\\.csv$",
"schema": "assets/schema_input.json",
"fa_icon": "fas fa-file-csv",
"help_text": "You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/viralrecon/docs/usage#introduction).",
"description": "Path to comma-separated file containing information about the samples you would like to analyse."
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},
"outdir": {
"type": "string",
"format": "directory-path",
"description": "The output directory where the results will be saved.",
"default": "./results",
"fa_icon": "fas fa-folder-open"
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"properties": {
"public_data_ids": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "\\.txt$",
"schema": "assets/schema_public_data_ids.json",
"description": "File containing SRA/ENA/GEO identifiers one per line in order to download their associated FastQ files.",
"fa_icon": "fas fa-database"
},
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},
"fasta": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "\\.fn?a(sta)?(\\.gz)?$",
"fa_icon": "fas fa-font",
"description": "Path to FASTA genome file.",
"help_text": "If you have no genome reference available, the pipeline can build one using a FASTA file. This requires additional time and resources, so it's better to use a pre-build index if possible."
},
"gff": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "\\.gff(\\.gz)?$",
"description": "Full path to GFF annotation file.",
"fa_icon": "fas fa-file-invoice"
},
"bowtie2_index": {
"type": "string",
"format": "path",
"description": "Path to directory or tar.gz archive for pre-built Bowtie2 index.",
"fa_icon": "fas fa-bezier-curve"
},
"primer_bed": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "\\.bed(\\.gz)?$",
"description": "If the '--protocol amplicon' parameter is provided then iVar is used to trim primer sequences after read alignment and before variant calling.",
"help_text": "iVar uses the primer positions relative to the viral genome supplied in this file to soft clip primer sequences from a coordinate sorted BAM file. The file must be in BED format as highlighted below:\n\n```\nMN908947.3 30 54 nCoV-2019_1_LEFT 60 -\nMN908947.3 385 410 nCoV-2019_1_RIGHT 60 +\nMN908947.3 320 342 nCoV-2019_2_LEFT 60 -\nMN908947.3 704 726 nCoV-2019_2_RIGHT 60 +\n```",
"fa_icon": "fas fa-stream"
},
"primer_fasta": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "\\.fn?a(sta)?(\\.gz)?$",
"description": "If the '--protocol amplicon' parameter is provided then Cutadapt is used to trim primer sequences from FastQ files before de novo assembly.",
"help_text": "This file must contain amplicon primer sequences in Fasta format. An example is shown below:\n\n```\n>nCoV-2019_1_LEFT\nACCAACCAACTTTCGATCTCTTGT\n>nCoV-2019_1_RIGHT\nCATCTTTAAGATGTTGACGTGCCTC\n>nCoV-2019_2_LEFT\nCTGTTTTACAGGTTCGCGACGT\n>nCoV-2019_2_RIGHT\nTAAGGATCAGTGCCAAGCTCGT\n```",
"fa_icon": "fas fa-stream"
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"properties": {
"fastq_dir": {
"type": "string",
"format": "directory-path",
"description": "Path to a folder containing fastq files from the Nanopore run.",
"help_text": "e.g. '--fastq_dir ./20191023_1522_MC-110615_0_FAO93606_12bf9b4f/fastq_pass/'.",
"fa_icon": "fas fa-folder-open"
},
"fast5_dir": {
"type": "string",
"format": "directory-path",
"description": "Path to a folder containing fast5 files from the Nanopore run.",
"help_text": "e.g. '--fast5_dir ./20191023_1522_MC-110615_0_FAO93606_12bf9b4f/fast5_pass/'. Not required when running the pipeline with the '--artic_minion_caller medaka' workflow.",
"fa_icon": "fas fa-folder-open"
},
"sequencing_summary": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"pattern": "\\.txt$",
"description": "Sequencing summary file generated after Nanopore run completion.",
"help_text": " e.g. '--sequencing_summary ./20191023_1522_MC-110615_0_FAO93606_12bf9b4f/sequencing_summary.txt'. Not required when running the pipeline with the '--artic_minion_caller medaka' workflow.",
"fa_icon": "fas fa-file"
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},
"multiqc_config": {
"type": "string",
"format": "file-path",
"mimetype": "text/plain",
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog",
"hidden": true
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"properties": {
"kraken2_db": {
"type": "string",
"format": "path",
"default": "s3://nf-core-awsmegatests/viralrecon/input_data/kraken2_human.tar.gz",
"fa_icon": "fab fa-gitkraken",
"description": "Full path to Kraken2 database built from host genome."
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},
"spades_hmm": {
"type": "string",
"format": "file-path",
"fa_icon": "fab fa-digg",
"description": "Path to profile HMMs specific for gene/organism to enhance SPAdes assembly."
},
"blast_db": {
"type": "string",
"format": "path",
"fa_icon": "fas fa-database",
"description": "Path to directory or tar.gz archive for pre-built BLAST database."
},
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},
"tracedir": {
"type": "string",
"format": "directory-path",
"description": "Directory to keep pipeline Nextflow logs and reports.",
"default": "${params.outdir}/pipeline_info",
"fa_icon": "fas fa-cogs",
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},
"custom_config_base": {
"type": "string",
"format": "directory-path",
"description": "Base directory for Institutional configs.",
"default": "https://raw.githubusercontent.com/nf-core/configs/master",
"hidden": true,
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