diff --git a/nextflow_schema.json b/nextflow_schema.json index 17c586c..499c94e 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,8 +1,9 @@ { "$schema": "http://json-schema.org/draft-07/schema", "$id": "https://raw.githubusercontent.com/./master/nextflow_schema.json", - "title": ". pipeline parameters", - "description": "", + "title": "epi2me-labs/wf-isoforms", + "description": "Isoform detection and characterisation.", + "url": "https://github.com/epi2me-labs/wf-isoforms", "type": "object", "definitions": { "basic_input_output_options": { @@ -18,7 +19,9 @@ }, "fastq": { "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": { "type": "string", @@ -26,6 +29,7 @@ }, "sample_sheet": { "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." }, "sanitize_fastq": { @@ -44,10 +48,12 @@ }, "ref_genome": { "type": "string", + "format": "file-path", "description": "Path to reference genome sequence [.fa/.fq/.fa.gz/fq.gz]" }, "ref_annotation": { "type": "string", + "format": "file-path", "description": "A reference annotation of gff format" }, "use_pychopper": { @@ -103,7 +109,7 @@ "default": " --conservative " }, "disable_ping": { - "type": "boolean" + "type": "boolean" } }, "required": [ @@ -176,4 +182,4 @@ "type": "boolean" } } -} \ No newline at end of file +}