Merge pull request #490 from nf-core/fix-code-block-rendering

fix code block in help text

Author: jasmezz

nextflow_schema.json

@@ -705,7 +705,7 @@
                 "amp_ampcombi_db": {
                     "type": "string",
                     "description": "The path to the folder containing the reference database files.",
-                    "help_text": "The path to the folder containing the reference database files (`*.fasta` and `*.tsv`); a fasta file and the corresponding table with structural, functional and if reported taxonomic classifications. AMPcombi will then generate the corresponding `mmseqs2` directory, in which all binary files are prepared for the downstream alignment of teh recovered AMPs with [MMseqs2](https://github.com/soedinglab/MMseqs2). These can also be provided by the user by setting up an mmseqs2 compatible database using `mmseqs createdb *.fasta` in a directory called `mmseqs2`.\n\nExample file structure for the reference database supplied by the user:\n\n```bash\namp_DRAMP_database/\n\u251c\u2500\u2500 general_amps_2024_11_13.fasta\n\u251c\u2500\u2500 general_amps_2024_11_13.txt\n\u2514\u2500\u2500 mmseqs2\n    \u251c\u2500\u2500 ref_DB\n    \u251c\u2500\u2500 ref_DB.dbtype\n    \u251c\u2500\u2500 ref_DB_h\n    \u251c\u2500\u2500 ref_DB_h.dbtype\n    \u251c\u2500\u2500 ref_DB_h.index\n    \u251c\u2500\u2500 ref_DB.index\n    \u251c\u2500\u2500 ref_DB.lookup\n    \u2514\u2500\u2500 ref_DB.source\n\nFor more information check the AMPcombi [documentation](https://ampcombi.readthedocs.io/en/main/usage.html#parse-tables)."
+                    "help_text": "The path to the folder containing the reference database files (`*.fasta` and `*.tsv`); a fasta file and the corresponding table with structural, functional and if reported taxonomic classifications. AMPcombi will then generate the corresponding `mmseqs2` directory, in which all binary files are prepared for the downstream alignment of teh recovered AMPs with [MMseqs2](https://github.com/soedinglab/MMseqs2). These can also be provided by the user by setting up an mmseqs2 compatible database using `mmseqs createdb *.fasta` in a directory called `mmseqs2`.\n\nExample file structure for the reference database supplied by the user:\n\n```bash\namp_DRAMP_database/\n\u251c\u2500\u2500 general_amps_2024_11_13.fasta\n\u251c\u2500\u2500 general_amps_2024_11_13.txt\n\u2514\u2500\u2500 mmseqs2\n    \u251c\u2500\u2500 ref_DB\n    \u251c\u2500\u2500 ref_DB.dbtype\n    \u251c\u2500\u2500 ref_DB_h\n    \u251c\u2500\u2500 ref_DB_h.dbtype\n    \u251c\u2500\u2500 ref_DB_h.index\n    \u251c\u2500\u2500 ref_DB.index\n    \u251c\u2500\u2500 ref_DB.lookup\n    \u2514\u2500\u2500 ref_DB.source```\n\nFor more information check the AMPcombi [documentation](https://ampcombi.readthedocs.io/en/main/usage.html#parse-tables)."
                 },
                 "amp_ampcombi_parsetables_cutoff": {
                     "type": "number",