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Add caveat about double/single quotes for build params
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@jfy133
jfy133 committed Dec 19, 2024
1 parent 590e51e commit 52cac91
Showing 1 changed file with 46 additions and 37 deletions.
83 changes: 46 additions & 37 deletions nextflow_schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -113,31 +113,67 @@
"description": "Turn on extending of Kraken2 database to include Bracken files. Requires nucleotide FASTA File input.",
"help_text": "Bracken2 databases are simply just a Kraken2 database with two additional files.\n\nNote however this requires a Kraken2 database _with_ intermediate files still in it, thus can result in large database directories."
},
"bracken_build_params": {
"type": "string",
"description": "Specify parameters being given to bracken build. Must be wrapped in double and single quotes: --bracken_build_params \"'--your_param'\"",
"help_text": "See [Bracken documentation](https://github.com/jenniferlu717/Bracken?tab=readme-ov-file#step-1-generate-the-bracken-database-file-databasexmerskmer_distrib)",
"fa_icon": "fas fa-users-cog"
},
"build_centrifuge": {
"type": "boolean",
"description": "Turn on building of Centrifuge database. Requires nucleotide FASTA file input.",
"fa_icon": "fas fa-toggle-on"
},
"centrifuge_build_params": {
"type": "string",
"description": "Specify parameters being given to centrifuge-build. Must be wrapped in double and single quotes: --centrifuge_build_params \"'--your_param'\"",
"help_text": "See [Centrifuge documentation](https://github.com/DaehwanKimLab/centrifuge/blob/master/MANUAL.markdown#database-download-and-index-building)",
"fa_icon": "fas fa-users-cog"
},
"build_diamond": {
"type": "boolean",
"fa_icon": "fas fa-toggle-on",
"description": "Turn on building of DIAMOND database. Requires amino-acid FASTA file input."
},
"diamond_build_params": {
"type": "string",
"description": "Specify parameters being given to diamond makedb. Must be wrapped in double and single quotes: --diamond_build_params \"'--your_param'\"",
"help_text": "See [diamond documentation](https://github.com/bbuchfink/diamond/wiki/3.-Command-line-options#makedb-options)",
"fa_icon": "fas fa-users-cog"
},
"build_ganon": {
"type": "boolean",
"description": "Turn on building of ganon database. Requires nucleotide FASTA file input.",
"fa_icon": "fas fa-toggle-on"
},
"ganon_build_params": {
"type": "string",
"description": "Specify parameters being given to ganon buildcustom. Must be wrapped in double and single quotes: --ganon_build_params \"'--your_param'\"",
"help_text": "See [ganon documentation](https://pirovc.github.io/ganon/custom_databases/)",
"fa_icon": "fas fa-users-cog"
},
"build_kaiju": {
"type": "boolean",
"description": "Turn on building of Kaiju database. Requires amino-acid FASTA file input.",
"fa_icon": "fas fa-toggle-on"
},
"kaiju_build_params": {
"type": "string",
"description": "Specify parameters being given to kaiju-mkbwt. Must be wrapped in double and single quotes: --kaiju_build_params \"'--your_param'\"",
"help_text": "See [Kaiju documentation](https://github.com/bioinformatics-centre/kaiju/tree/master#custom-database)",
"fa_icon": "fas fa-users-cog"
},
"build_kraken2": {
"type": "boolean",
"description": "Turn on building of Kraken2 database. Requires nucleotide FASTA file input.",
"fa_icon": "fas fa-toggle-on"
},
"kraken2_build_params": {
"type": "string",
"description": "Specify parameters being given to kraken2 build. Must be wrapped in double and single quotes: --kraken2_build_params \"'--your_param'\"",
"help_text": "See [Kraken2 documentation](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown#custom-databases)",
"fa_icon": "fas fa-users-cog"
},
"kraken2_keepintermediate": {
"type": "boolean",
"fa_icon": "fas fa-save",
Expand All @@ -148,50 +184,23 @@
"fa_icon": "fas fa-toggle-on",
"description": "Turn on building of KrakenUniq database. Requires nucleotide FASTA file input."
},
"krakenuniq_build_params": {
"type": "string",
"description": "Specify parameters being given to krakenuniq build. Must be wrapped in double and single quotes: --krakenuniq_build_params \"'--your_param'\"",
"help_text": "See [KrakenUniq documentation](https://github.com/fbreitwieser/krakenuniq?tab=readme-ov-file#database-building)",
"fa_icon": "fas fa-users-cog"
},
"build_malt": {
"type": "boolean",
"fa_icon": "fas fa-toggle-on",
"description": "Turn on building of MALT database. Requires nucleotide FASTA file input."
},
"bracken_build_params": {
"type": "string",
"description": "Specify parameters being given to bracken build",
"help_text": "See [Bracken documentation](https://github.com/jenniferlu717/Bracken?tab=readme-ov-file#step-1-generate-the-bracken-database-file-databasexmerskmer_distrib)"
},
"centrifuge_build_params": {
"type": "string",
"description": "Specify parameters being given to centrifuge-build",
"help_text": "See [Centrifuge documentation](https://github.com/DaehwanKimLab/centrifuge/blob/master/MANUAL.markdown#database-download-and-index-building)"
},
"diamond_build_params": {
"type": "string",
"description": "Specify parameters being given to diamond makedb",
"help_text": "See [diamond documentation](https://github.com/bbuchfink/diamond/wiki/3.-Command-line-options#makedb-options)"
},
"ganon_build_params": {
"type": "string",
"description": "Specify parameters being given to ganon buildcustom",
"help_text": "See [ganon documentation](https://pirovc.github.io/ganon/custom_databases/)"
},
"kaiju_build_params": {
"type": "string",
"description": "Specify parameters being given to kaiju-mkbwt",
"help_text": "See [Kaiju documentation](https://github.com/bioinformatics-centre/kaiju/tree/master#custom-database)"
},
"kraken2_build_params": {
"type": "string",
"description": "Specify parameters being given to kraken2 build",
"help_text": "See [Kraken2 documentation](https://github.com/DerrickWood/kraken2/blob/master/docs/MANUAL.markdown#custom-databases)"
},
"krakenuniq_build_params": {
"type": "string",
"description": "Specify parameters being given to krakenuniq build",
"help_text": "See [KrakenUniq documentation](https://github.com/fbreitwieser/krakenuniq?tab=readme-ov-file#database-building)"
},
"malt_build_params": {
"type": "string",
"description": "Specify parameters given to malt-build. Must include --sequenceType DNA or Protein.",
"help_text": "At least the type of reference sequences should be specified. (For RNA sequences, use the DNA setting) - from [MALT manual](https://software-ab.cs.uni-tuebingen.de/download/malt/)."
"description": "Specify parameters given to malt-build. Must include --sequenceType DNA or Protein and be wrapped in double and single quotes: --malt_build_params \"'--sequenceType DNA --your_param'\"",
"help_text": "At least the type of reference sequences should be specified. (For RNA sequences, use the DNA setting) - from [MALT manual](https://software-ab.cs.uni-tuebingen.de/download/malt/).",
"default": "--sequenceType DNA",
"fa_icon": "fas fa-users-cog"
}
},
"fa_icon": "fas fa-database"
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