diff --git a/nextflow_schema.json b/nextflow_schema.json index 56785f0e..0dc716b1 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -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": { @@ -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, @@ -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.",