Apply rnaseq -> riboseq fixes from code review

Co-authored-by: Maxime U Garcia <[email protected]>

modules/local/gtf_filter/main.nf

@@ -17,7 +17,7 @@ process GTF_FILTER {
     when:
     task.ext.when == null || task.ext.when
 
-    script: // filter_gtf.py is bundled with the pipeline, in nf-core/rnaseq/bin/
+    script: // filter_gtf.py is bundled with the pipeline, in nf-core/riboseq/bin/
     """
     filter_gtf.py \\
         --gtf $gtf \\

nextflow_schema.json

@@ -1,8 +1,8 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "https://raw.githubusercontent.com/nf-core/rnaseq/master/nextflow_schema.json",
-    "title": "nf-core/rnaseq pipeline parameters",
-    "description": "RNA sequencing analysis pipeline for gene/isoform quantification and extensive quality control.",
+    "$id": "https://raw.githubusercontent.com/nf-core/riboseq/master/nextflow_schema.json",
+    "title": "nf-core/riboseq pipeline parameters",
+    "description": "Analysis of ribosome profiling, or Ribo-Seq (also named ribosome footprinting)",
     "type": "object",
     "definitions": {
         "input_output_options": {
@@ -20,7 +20,7 @@
                     "pattern": "^\\S+\\.csv$",
                     "schema": "assets/schema_input.json",
                     "description": "Path to comma-separated file containing information about the samples in the experiment.",
-                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 4 columns, and a header row. See [usage docs](https://nf-co.re/rnaseq/usage#samplesheet-input).",
+                    "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/riboseq/usage#samplesheet-input).",
                     "fa_icon": "fas fa-file-csv"
                 },
                 "outdir": {