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de-duplicating txp2gene args (lint complains)
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gennadyFauna committed Feb 13, 2024
1 parent 752d051 commit 4d90d60
Showing 1 changed file with 6 additions and 12 deletions.
18 changes: 6 additions & 12 deletions nextflow_schema.json
Original file line number Diff line number Diff line change
Expand Up @@ -138,7 +138,12 @@
"default": "s3://ngi-igenomes/igenomes",
"fa_icon": "fas fa-cloud-download-alt",
"hidden": true
}
},
"txp2gene": {
"type": "string",
"description": "Kallisto or Alevin gene mapping file.",
"fa_icon": "fas map-marked-alt"
},
}
},
"alevin_options": {
Expand All @@ -152,12 +157,6 @@
"description": "This can be used to specify a precomputed Salmon index in the pipeline, in order to skip the generation of required indices by Salmon itself.",
"fa_icon": "fas fa-fish"
},
"txp2gene": {
"type": "string",
"description": "Path to transcript to gene mapping file. This allows the specification of a transcript to gene mapping file for Salmon Alevin and AlevinQC.",
"help_text": "> This is the same as the `kallisto_gene_map` parameter below.",
"fa_icon": "fas fa-map-marked-alt"
},
"simpleaf_rlen": {
"type": "integer",
"default": 91,
Expand Down Expand Up @@ -208,11 +207,6 @@
"description": "Specify a path to the precomputed Kallisto index.",
"fa_icon": "fas fa-rainbow"
},
"txp2gene": {
"type": "string",
"description": "Specify a Kallisto gene mapping file here. If you don't, this will be automatically created in the Kallisto workflow when specifying a valid `--gtf` file.",
"fa_icon": "fas fa-rainbow"
},
"kb_t1c": {
"type": "string",
"description": "Specify a path to the cDNA transcripts-to-capture.",
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