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Update nextflow_schema.json

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Thomas Rich 2022-01-11 16:04:22 +00:00
parent de3edcb31e
commit 151ef46522
1 changed files with 11 additions and 5 deletions
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nextflow_schema.json
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@ -1,8 +1,9 @@
{ {
"$schema": "http://json-schema.org/draft-07/schema", "$schema": "http://json-schema.org/draft-07/schema",
"$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json",
"title": ". pipeline parameters", "title": "epi2me-labs/wf-isoforms",
"description": "", "description": "Isoform detection and characterisation.",
"url": "https://github.com/epi2me-labs/wf-isoforms",
"type": "object", "type": "object",
"definitions": { "definitions": {
"basic_input_output_options": { "basic_input_output_options": {
@ -18,7 +19,9 @@
}, },
"fastq": { "fastq": {
"type": "string", "type": "string",
"description": "Directory containing fastq input files. May contain fastq files directly or directories name barcodeXX relating to independent samples." "format": "path",
"description": "A fastq file or directory containing fastq input files or directories of input files.",
"help_text": "If directories named \\\"barcode*\\\" are found under the `--fastq` directory the data is assumed to be multiplex and each barcode directory will be processed independently. If `.fastq(.gz)` files are found under the `--fastq` directory the sample is assumed to not be multiplexed. In this second case `--samples` should be a simple name rather than a CSV file."
}, },
"sample": { "sample": {
"type": "string", "type": "string",
@ -26,6 +29,7 @@
}, },
"sample_sheet": { "sample_sheet": {
"type": "string", "type": "string",
"format": "file-path",
"description": "CSV file with columns named `barcode`, `sample_name` and `type`. Permissible if passing a directory containing barcodeXX sub-directories." "description": "CSV file with columns named `barcode`, `sample_name` and `type`. Permissible if passing a directory containing barcodeXX sub-directories."
}, },
"sanitize_fastq": { "sanitize_fastq": {
@ -44,10 +48,12 @@
}, },
"ref_genome": { "ref_genome": {
"type": "string", "type": "string",
"format": "file-path",
"description": "Path to reference genome sequence [.fa/.fq/.fa.gz/fq.gz]" "description": "Path to reference genome sequence [.fa/.fq/.fa.gz/fq.gz]"
}, },
"ref_annotation": { "ref_annotation": {
"type": "string", "type": "string",
"format": "file-path",
"description": "A reference annotation of gff format" "description": "A reference annotation of gff format"
}, },
"use_pychopper": { "use_pychopper": {