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fix code block in help text #490

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jasmezz merged 1 commit into from
Jul 28, 2025
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fix code block in help text #490

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2 changes: 1 addition & 1 deletion nextflow_schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -708,7 +708,7 @@
"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",
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