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fix validation issues with meta-schema #77

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merged 1 commit into from
Jan 19, 2024
Merged

fix validation issues with meta-schema #77

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12 changes: 6 additions & 6 deletions assets/nf-params.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -107,15 +107,15 @@
## Remove duplicated reads (exact same sequence)
## Type: boolean
## -----------------------------------------------------------------------------
# dedup = false
# dedup = null

## -----------------------------------------------------------------------------
## remove_polyg
## -----------------------------------------------------------------------------
## Remove PolyG sequences (length of 10 or more)
## Type: boolean
## -----------------------------------------------------------------------------
# remove_polyg = false
# remove_polyg = null


## =============================================================================
Expand Down Expand Up @@ -271,7 +271,7 @@
## Skip analysis step
## Type: boolean
## -----------------------------------------------------------------------------
# skip_analysis = false
# skip_analysis = null

## -----------------------------------------------------------------------------
## compute_polarization
Expand All @@ -296,7 +296,7 @@
## computing polarization, coabundance and colocalization scores
## Type: boolean
## -----------------------------------------------------------------------------
# use_full_bipartite = false
# use_full_bipartite = null

## -----------------------------------------------------------------------------
## polarization_normalization
Expand All @@ -313,7 +313,7 @@
## polarization
## Type: boolean
## -----------------------------------------------------------------------------
# polarization_binarization = false
# polarization_binarization = null

## -----------------------------------------------------------------------------
## colocalization_transformation
Expand Down Expand Up @@ -362,7 +362,7 @@
## Skip report generation
## Type: boolean
## -----------------------------------------------------------------------------
# skip_report = false
# skip_report = null


## =============================================================================
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28 changes: 14 additions & 14 deletions nextflow_schema.json
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Original file line number Diff line number Diff line change
Expand Up @@ -90,19 +90,18 @@
"dedup": {
"fa_icon": "fas clone",
"description": "Remove duplicated reads (exact same sequence)",
"type": "boolean",
"default": false
"type": "boolean"
},
"remove_polyg": {
"fa_icon": "fas g",
"description": "Remove PolyG sequences (length of 10 or more)",
"type": "boolean",
"default": false
"type": "boolean"
}
}
},
"adapterqc_options": {
"title": "Adapter QC Options",
"type": "object",
"properties": {
"adapterqc_mismatches": {
"fa_icon": "fas not-equal",
Expand All @@ -116,6 +115,7 @@
},
"demux_options": {
"title": "Demux options",
"type": "object",
"properties": {
"demux_mismatches": {
"fa_icon": "fas not-equal",
Expand All @@ -135,9 +135,10 @@
},
"collapse_options": {
"title": "Collapse options",
"type": "object",
"properties": {
"markers_ignore": {
"fa-icon": "fas fa-list",
"fa_icon": "fas fa-list",
"description": "A list of comma separated antibodies to discard",
"type": "string",
"pattern": "(\\S+)?(,\\S+)*"
Expand Down Expand Up @@ -181,6 +182,7 @@
},
"graph_options": {
"title": "Options for pixelator graph command.",
"type": "object",
"properties": {
"multiplet_recovery": {
"description": "Activate the multiplet recovery using leiden community detection",
Expand Down Expand Up @@ -209,6 +211,7 @@
},
"annotate_options": {
"title": "Options for pixelator annotate command.",
"type": "object",
"properties": {
"min_size": {
"description": "The minimum size (pixels) a component/cell can have (disabled by default)",
Expand All @@ -233,11 +236,11 @@
},
"analysis_options": {
"title": "Options for pixelator analysis command.",
"type": "object",
"properties": {
"skip_analysis": {
"description": "Skip analysis step",
"type": "boolean",
"default": false
"type": "boolean"
},
"compute_polarization": {
"description": "Compute polarization scores matrix (clusters by markers)",
Expand All @@ -251,8 +254,7 @@
},
"use_full_bipartite": {
"description": "Use the bipartite graph instead of the one-node projection when computing polarization, coabundance and colocalization scores",
"type": "boolean",
"default": false
"type": "boolean"
},
"polarization_normalization": {
"description": "Which approach to use to normalize the antibody counts.",
Expand All @@ -264,8 +266,7 @@
"polarization_binarization": {
"fa_icon": "fas binary",
"description": "Transform the antibody counts to 0-1 (binarize) when computing polarization",
"type": "boolean",
"default": false
"type": "boolean"
},
"colocalization_transformation": {
"type": "string",
Expand Down Expand Up @@ -295,11 +296,11 @@
},
"report_options": {
"title": "Options for pixelator report command.",
"type": "object",
"properties": {
"skip_report": {
"description": "Skip report generation",
"type": "boolean",
"default": false
"type": "boolean"
}
}
},
Expand All @@ -310,7 +311,6 @@
"properties": {
"pixelator_container": {
"type": "string",
"format": "url",
"description": "Override the container image reference to use for all steps using the `pixelator` command.",
"help_text": "Use this to force the pipeline to use a different image version in all steps that use the pixelator command.\nThe pipeline is not garanteed to work when using different pixelator versions."
}
Expand Down