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Chore/fix json schema types #184

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176e073
Fix types in json schemas
johandahlberg Feb 11, 2026
90b51ec
Schema touch-ups with creation tool
johandahlberg Feb 12, 2026
7236f59
Update CHANGELOG
johandahlberg Feb 12, 2026
20b3a9d
Update CHANGELOG.md
johandahlberg Feb 17, 2026
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8 changes: 6 additions & 2 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -7,11 +7,15 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Changed

- Set default pna_graph_component_size_min_threshold to 8000 instead of null (i.e. automatic).
- Set default pna_graph_component_size_min_threshold to 8000 instead of null (i.e. automatic) by @ptajvar [#183](https://github.com/nf-core/pixelator/pull/183).

### Removed

- Support for MPX in the pipeline
- Support for MPX in the pipeline by @johandahlberg [#182](https://github.com/nf-core/pixelator/pull/182)

### Enhancements & fixes

- Update schema files (e.g. expliclitly use integer types for integers, rather than numbers) by @johandahlberg [#184](https://github.com/nf-core/pixelator/pull/184)

## [[2.3.1](https://github.com/nf-core/pixelator/releases/tag/2.3.1)] - 2025-01-14

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32 changes: 18 additions & 14 deletions assets/schema_input.json
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Expand Up @@ -7,45 +7,49 @@
"items": {
"type": "object",
"required": ["sample", "design", "fastq_1"],
"additionalProperties": false,
"properties": {
"sample": {
"type": "string",
"pattern": "^\\S+$",
"errorMessage": "Sample name must be provided and cannot contain spaces",
"description": "Sample name (no spaces).",
"meta": ["id"]
},
"design": {
"type": "string",
"meta": ["design"],
"errorMessage": "Design must be specified"
"pattern": "^\\S+$",
"errorMessage": "Design must be specified",
"description": "Design identifier (no spaces).",
"meta": ["design"]
},
"panel": {
"errorMessage": "Panel name must be specified",
"type": "string",
"pattern": "^\\S+$",
"description": "Panel identifier (no spaces).",
"errorMessage": "panel or panel_file must be specified",
"meta": ["panel"]
},
"panel_file": {
"type": "string",
"format": "file-path",
"description": "Optional panel file path. Empty string allowed. If set, must end with .csv, .tsv, .yaml, or .yml and contain no spaces.",
"errorMessage": "Panel file must either be left empty or cannot contain spaces and must have extension '.csv', '.tsv' or '.yaml'",
"anyOf": [
{
"type": "string",
"pattern": "^\\S+.(csv|tsv|ya?ml)$"
},
{
"type": "string",
"maxLength": 0
}
]
"pattern": "^$|^\\S+\\.(csv|tsv|ya?ml)$"
},
"fastq_1": {
"type": "string",
"format": "file-path",
"pattern": "^\\S+\\.f(ast)?q\\.gz$",
"description": "FASTQ(.gz) path for read 1 (no spaces).",
"errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
},
"fastq_2": {
"type": "string",
"format": "file-path",
"pattern": "^\\S+\\.f(ast)?q\\.gz$",
"errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'"
"errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'",
"description": "Optional FASTQ(.gz) path for read 2 (no spaces)."
}
}
}
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63 changes: 28 additions & 35 deletions nextflow_schema.json
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Expand Up @@ -52,20 +52,21 @@
"save_pna_amplicon_reads": {
"fa_icon": "fas fa-save",
"type": "boolean",
"default": false,
"description": "Save intermediate amplicon reads generated from the raw input reads.",
"help": "By default, generated amplicon FastQ files will not be saved to the results directory. Specify this flag (or set it to `true` in your config file) to copy these files to the results directory when complete."
},
"pna_amplicon_mismatches": {
"type": "number",
"minimum": 0.0,
"minimum": 0,
"maximum": 0.5,
"description": "The number of mismatches allowed while anchoring reads using LBS sequences (in percentage of seen LBS length) [default: 0.1; 0.0<=x<=0.5]"
"description": "The number of mismatches allowed while anchoring reads using LBS sequences (in percentage of seen LBS length) [default: 0.1; 0.0<=x<=0.5]",
"default": 0.1
},
"pna_amplicon_remove_polyg": {
"fa_icon": "fas g",
"description": "Remove PolyG sequences (length of 10 or more)",
"type": "boolean"
"type": "boolean",
"default": true
},
"pna_amplicon_quality_cutoff": {
"fa_icon": "fas gauge",
Expand All @@ -82,7 +83,7 @@
"type": "number",
"default": 0.8,
"minimum": 0.5,
"maximum": 1.0,
"maximum": 1,
"description": "The threshold for determining if a UMI sequence is of low complexity and will be removed. [0.5<=x<=1.0]"
},
"pna_amplicon_lbs_filter": {
Expand All @@ -100,8 +101,8 @@
"pna_amplicon_lbs_filter_error_rate": {
"type": "number",
"default": 0.1,
"minimum": 0.0,
"maximum": 1.0,
"minimum": 0,
"maximum": 1,
"description": "The allowed error-rate in a semi-global alignment of a UMI sequence with the LBS regions. The error rate is defined as a percentage of UMI length. [0.0<=x<=1.0]"
}
}
Expand All @@ -113,7 +114,7 @@
"pna_demux_mismatches": {
"fa_icon": "fas not-equal",
"description": "The number of mismatches allowed in marker barcodes.",
"type": "number",
"type": "integer",
"default": 1,
"minimum": 0,
"maximum": 2
Expand All @@ -127,7 +128,7 @@
},
"pna_demux_output_max_chunks": {
"fa_icon": "fas fa-arrows-alt-h",
"type": "number",
"type": "integer",
"minimum": 1,
"maximum": 32,
"default": 8,
Expand All @@ -145,21 +146,18 @@
"save_pna_demux_parquet": {
"fa_icon": "fas fa-save",
"type": "boolean",
"default": false,
"description": "Save intermediate parquet files containing embeddings of all reads that contain valid antibody barcodes.",
"help": "By default, parquet files containing embeddings of reads with valid antibody barcodes will not be saved to the results directory. Specify this flag (or set to `true` in your config file) to copy these files to the results directory when complete."
},
"save_pna_demux_passed_reads": {
"fa_icon": "fas fa-save",
"type": "boolean",
"default": false,
"description": "Save intermediate FASTQC read files containing all reads that contain valid antibody barcodes.",
"help": "By default, FastQ files containing reads with valid antibody barcodes will not be saved to the results directory. Specify this flag (or set to `true` in your config file) to copy these files to the results directory when complete."
},
"save_pna_demux_failed_reads": {
"fa_icon": "fas fa-save",
"type": "boolean",
"default": false,
"description": "Save intermediate FASTQC read files containing all reads that do not contain valid antibody barcodes.",
"help": "By default, FastQ files containing reads without valid antibody barcodes will not be saved to the results directory. Specify this flag (or set to `true` in your config file) to copy these files to the results directory when complete."
}
Expand All @@ -175,7 +173,7 @@
"default": "directional",
"enum": ["cluster", "directional"],
"type": "string",
"help": "**cluster:** Form networks of connected UMIs (based on hamming distance threshold). Each connected component is a read group. In the above example, all the UMIs are contained in a single connected component and thus there is one read group containing all reads, with ACGT as the ‘selected’ UMI.\n\n**directional (default):** Form networks with edges defined based on hamming distance threshold and node A counts >= (2 * node B counts) - 1. Each connected component is a read group, with the node with the highest counts selected as the top node for the component."
"help": "**cluster:** Form networks of connected UMIs (based on hamming distance threshold). Each connected component is a read group. In the above example, all the UMIs are contained in a single connected component and thus there is one read group containing all reads, with ACGT as the `selected` UMI.\n\n**directional (default):** Form networks with edges defined based on hamming distance threshold and node A counts >= (2 * node B counts) - 1. Each connected component is a read group, with the node with the highest counts selected as the top node for the component."
},
"pna_collapse_mismatches": {
"fa_icon": "fas not-equal",
Expand All @@ -188,7 +186,6 @@
"save_pna_collapsed_reads": {
"fa_icon": "fas fa-save",
"type": "boolean",
"default": false,
"description": "Save an intermediate parquet file containing collapsed read information.",
"help": "By default, intermediate collapsed reads will not be saved to the results directory. Specify this flag (or set to `true` in your config file) to copy these files to the results directory when complete."
}
Expand All @@ -200,7 +197,6 @@
"properties": {
"save_pna_graph_pixelfile": {
"type": "boolean",
"default": false,
"description": "Save the PXL dataset after the graph stage.",
"help": "By default, the PXL file after graph will not be saved to the results directory unless `--skip_analysis` and `--skip_layout` is passed. Specify this flag (or set to `true` in your config file) to copy these files to the results directory when complete."
},
Expand All @@ -210,21 +206,21 @@
"default": true
},
"pna_graph_leiden_iterations": {
"type": "number",
"type": "integer",
"default": 1,
"description": "Number of iterations for the leiden algorithm.",
"help": "High values will decrease the variance of the results but increase the runtime"
},
"pna_graph_initial_stage_leiden_resolution": {
"default": 1.0,
"minimum": 0.0,
"default": 1,
"minimum": 0,
"type": "number",
"description": "The resolution parameter for the leiden algorithm at the initial stage.",
"help": "This should typically be set higher than the refinement stage resolution."
},
"pna_graph_refinement_stage_leiden_resolution": {
"default": 0.01,
"minimum": 0.0,
"minimum": 0,
"type": "number",
"description": "The resolution parameter for the leiden algorithm at the refinement stage.",
"help": "This should typically be set lower than the initial stage resolution."
Expand All @@ -237,47 +233,47 @@
"description": "Discard edges with a read count below given value. Set to 1 to disable filtering."
},
"pna_graph_min_component_size_in_refinement": {
"type": "number",
"type": "integer",
"default": 1000,
"minimum": 1,
"description": "The minimum component size to consider for refinement"
},
"pna_graph_max_refinement_recursion_depth": {
"type": "number",
"type": "integer",
"default": 5,
"minimum": 1,
"maximum": 100,
"description": "The maximum recursion depth for the refinement algorithm. Set to 1 to disable refinement."
},
"pna_graph_initial_stage_max_edges_to_remove": {
"type": "number",
"type": "integer",
"minimum": 1,
"description": "The maximum number of edges to remove between components during the initial stage (iteration == 0) of multiplet recovery."
},
"pna_graph_refinement_stage_max_edges_to_remove": {
"type": "number",
"type": "integer",
"default": 4,
"minimum": 1,
"description": "The maximum number of edges to remove between components during the refinement stage (iteration > 0) of multiplet recovery."
},
"pna_graph_initial_stage_max_edges_to_remove_relative": {
"type": "number",
"minimum": 0.0,
"minimum": 0,
"description": "The maximum number of edges to remove between two components relative to the number of nodes in the smaller of the two when during the initial stage (iteration == 0) of multiplet recovery."
},
"pna_graph_refinement_stage_max_edges_to_remove_relative": {
"type": "number",
"minimum": 0.0,
"minimum": 0,
"description": "The maximum number of edges to remove between two components relative to the number of nodes in the smaller of the two when during the refinement stage (iteration > 0) of multiplet recovery."
},
"pna_graph_graph_min_component_size_to_prune": {
"type": "number",
"type": "integer",
"minimum": 1,
"default": 100,
"description": "The minimum number of nodes in an potential new components in order for it to be pruned."
},
"pna_graph_component_size_min_threshold": {
"type": "number",
"type": "integer",
"minimum": 1,
"default": 8000,
"description": "Components with fewer nodes than this will be filtered from the output data. Set to null to enable automatic size filtering based on the data."
Expand All @@ -295,7 +291,6 @@
"save_pna_denoise_pixelfile": {
"fa_icon": "fas fa-save",
"type": "boolean",
"default": false,
"description": "Save the PXL dataset after the denoise stage.",
"help": "By default, the PXL file after denoise will not be saved to the results directory."
},
Expand All @@ -308,13 +303,13 @@
"type": "number",
"description": "The p-value threshold for the a marker to be considered significantly over-expressed in the one-core layer of a component",
"default": 0.05,
"minimum": 0.0
"minimum": 0
},
"pna_denoise_inflate_factor": {
"type": "number",
"description": "The inflate factor for the number of nodes from over-expressed markers to be removed from the one-core layer of a component",
"default": 1.5,
"minimum": 1.0
"minimum": 1
}
}
},
Expand All @@ -329,7 +324,6 @@
"save_pna_analysis_pixelfile": {
"fa_icon": "fas fa-save",
"type": "boolean",
"default": false,
"description": "Save the PXL dataset after the analysis stage.",
"help": "By default, the PXL dataset after the analysis stage will only be saved be saved when `--skip_layout` is passed. Specify this flag (or set to `true` in your config file) to copy these files to the results directory when complete."
},
Expand All @@ -340,7 +334,8 @@
},
"pna_analysis_compute_k_cores": {
"description": "Compute k-core summary tables for each component",
"type": "boolean"
"type": "boolean",
"default": true
},
"pna_analysis_proximity_nbr_of_permutations": {
"type": "integer",
Expand Down Expand Up @@ -372,8 +367,7 @@
},
"pna_layout_no_node_marker_counts": {
"description": "Skip adding marker counts to the layout.",
"type": "boolean",
"default": false
"type": "boolean"
},
"pna_layout_layout_algorithm": {
"description": "Select a layout algorithm to use. This can be specified as a comma separated list to compute multiple layouts. Possible values are: pmds, pmds_3d, wpmds, wpmds_3d.",
Expand Down Expand Up @@ -419,7 +413,6 @@
"save_all": {
"fa_icon": "fas fa-save",
"type": "boolean",
"default": false,
"description": "Save all intermediate results.",
"help": "This option is equivalent of passing all: `--save_* and --save_pna_*` options."
},
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