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Merged
merged 5 commits into from
Apr 16, 2025
Merged

Json schema improvements #592

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3c8875e
initial edits of schema
microlei Mar 25, 2025
bffa5a3
updated changelog
microlei Mar 25, 2025
38a931b
updated changelog and added exists
microlei Mar 25, 2025
cf63a6f
[automated] Fix code linting
nf-core-bot Apr 16, 2025
c6f0eeb
Update CHANGELOG.md
jfy133 Apr 16, 2025
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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -9,6 +9,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Fixed`

- [592](https://github.com/nf-core/taxprofiler/pull/592) improved json schema (by @microlei)

### `Dependencies`

### `Deprecated`
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9 changes: 8 additions & 1 deletion nextflow_schema.json
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Expand Up @@ -340,18 +340,23 @@
},
"hostremoval_reference": {
"type": "string",
"format": "file-path",
"exists": true,
"fa_icon": "fas fa-file-alt",
"description": "Specify path to single reference FASTA of host(s) genome(s)",
"help_text": "Specify a path to the FASTA file (optionally gzipped) of the reference genome of the organism to be removed.\n\nIf you have two or more host organisms or contaminants you wish to remove, you can concatenate the FASTAs of the different taxa into a single one to provide to the pipeline."
},
"shortread_hostremoval_index": {
"type": "string",
"format": "directory-path",
"fa_icon": "fas fa-address-book",
"description": "Specify path to the directory containing pre-made BowTie2 indexes of the host removal reference",
"help_text": "Specify the path to a _directory_ containing pre-made Bowtie2 reference index files (i.e. the directory containing `.bt1`, `.bt2` files etc.). These should sit in the same directory alongside the the reference file specified in `--hostremoval_reference`.\n\nSpecifying premade indices can speed up runtime of the host-removal step, however if not supplied the pipeline will generate the indices for you."
},
"longread_hostremoval_index": {
"type": "string",
"format": "file-path",
"exists": true,
"fa_icon": "fas fa-address-book",
"description": "Specify path to a pre-made Minimap2 index file (.mmi) of the host removal reference",
"help_text": "Specify path to a pre-made Minimap2 index file (.mmi) of the host removal reference file given to `--hostremoval_reference`.\n\nSpecifying a premade index file can speed up runtime of the host-removal step, however if not supplied the pipeline will generate the indices for you."
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"malt_mode": {
"type": "string",
"default": "BlastN",
"enum": ["Unknown", "BlastN", "BlastP", "BlastX", "Classifier"],
"fa_icon": "fas fa-check-square",
"description": "Specify which MALT alignment mode to use",
"help_text": "Specify which version of MALT alignment to use.\n\nBlastN is generally recommended (nucleotide-nucleotide alignment), but particularly for very short reads (such as aDNA), whereas BlastX mode is similar to DIAMOND and will translate the nucleotide to amino acid sequences. Note each type of alignment mode requires different parameters during database construction. Refer to the MALT manual for more information.\n\n> Modifies tool parameter(s):\n> - malt-run: `-mode` "
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"ganon_report_type": {
"type": "string",
"default": "reads",
"enum": ["abundance", "reads", "matches", "dist", "corr"],
"description": "Specify the type of ganon report to save.",
"help_text": "Specify the type of taxonomic report to produce from ganon report. This mainly refers to which form of 'value' to print: raw read counts, abundance estimates, genome-size normalised etc. \n\nSee the [ganon documentation](https://pirovc.github.io/ganon/outputfiles/#ganon-report) for more information of each option.\n\n> Modifies tool parameter(s):\n- ganon report: `--report-type`\n",
"enum": ["abundance", "reads", "matches", "dist", "corr"],
"fa_icon": "fas fa-file"
},
"ganon_report_rank": {
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"multiqc_config": {
"type": "string",
"format": "file-path",
"exists": true,
"description": "Custom config file to supply to MultiQC.",
"fa_icon": "fas fa-cog",
"hidden": true
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