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Merge branch 'update-schema' into 'dev'

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Update nextflow_schema.json

See merge request epi2melabs/workflow-containers/wf-isoforms!32
This commit is contained in:
Thomas Rich 2022-01-11 16:04:22 +00:00
commit 391b5d5c84
1 changed files with 11 additions and 5 deletions
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nextflow_schema.json
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@ -1,8 +1,9 @@
{
"$schema": "http://json-schema.org/draft-07/schema",
"$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"
}
}
}
}