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James A. Fellows Yates 2022-12-20 21:48:08 +01:00 committed by GitHub
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2
nextflow.config
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@ -38,7 +38,7 @@ params {
version = false version = false
validate_params = true validate_params = true
show_hidden_params = false show_hidden_params = false
schema_ignore_params = 'genomes' schema_ignore_params = 'genomes,fasta'
// Config options // Config options

9
nextflow_schema.json
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@ -712,15 +712,6 @@
"help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details.", "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details.",
"hidden": true "hidden": true
}, },
"fasta": {
"type": "string",
"description": "Path to FASTA genome file.",
"help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.",
"pattern": "^\\\\S+\\\\.fn?a(sta)?(\\\\.gz)?$",
"format": "file-path",
"mimetype": "text/plain",
"fa_icon": "far fa-file-code"
},
"igenomes_base": { "igenomes_base": {
"type": "string", "type": "string",
"format": "directory-path", "format": "directory-path",