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add long_phase supplementary alignment tag to extended args #163

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add long_phase supplementary alignment tag to extended args #163

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c14136d
add long_phase supplementary alignment tag
AmberVerhasselt Apr 29, 2026
14b14c7
fix schema
AmberVerhasselt Apr 29, 2026
c0e3ab2
fix schema 2.0
AmberVerhasselt Apr 29, 2026
af57f20
fix schema 3.0
AmberVerhasselt Apr 29, 2026
f4e7cc0
fix schema 4.0
AmberVerhasselt Apr 29, 2026
bb3199d
fix schema 5.0
AmberVerhasselt Apr 29, 2026
be64ce5
fix schema 6.0
AmberVerhasselt Apr 30, 2026
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5 changes: 5 additions & 0 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -374,6 +374,11 @@ process {
}
withName: '.*:LONGPHASE_HAPLOTAG*' {
ext.prefix = { "${meta.id}_${meta.type}" }
ext.args = {
[
params.longphase_tag_supplementary ? "--tagSupplementary" : ''
].join(' ').trim()
}
publishDir = [
path: { "${params.outdir}/${meta.id}/bamfiles" },
mode: params.publish_dir_mode,
Expand Down
8 changes: 7 additions & 1 deletion docs/usage.md
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Expand Up @@ -152,6 +152,12 @@ If you want to run with a CHM13 reference without using `--genome CHM13` (for ex
| `--skip_modkit` | A boolean to skip the modkit pileup step. Default = `false` |
| `--skip_whatshapstats` | A boolean to skip WhatsHap phasing statistics. Default = `false` |

#### LONGPHASE options:

| Parameter | Description |
| ------------------------------- | ---------------------------------------------------------------------------------- |
| `--longphase_tag_supplementary` | Include supplementary alignments in Longphase haplotype tagging. Default = `false` |

#### VEP options:

| Parameter | Description |
Expand Down Expand Up @@ -200,7 +206,7 @@ If you want to run with a CHM13 reference without using `--genome CHM13` (for ex

| Parameter | Description |
| ---------------------- | ------------------------------------------------------------------------------------ |
| `--severus_minsupport` | Minimum number of supporting reads required for SEVERUS to call an SV. Default = `5` |
| `--severus_minsupport` | Minimum number of supporting reads required for SEVERUS to call an SV. Default = `3` |

#### WAKHAN Options

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3 changes: 3 additions & 0 deletions nextflow.config
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Expand Up @@ -22,6 +22,9 @@ params {
prioritize_caller_somatic = 'deepsomatic'
generate_gvcf = false

// Longphase options
longphase_tag_supplementary = false

// PON Options
clairsto_pon_vcfs = null
clairsto_pon_flags = null
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58 changes: 30 additions & 28 deletions nextflow_schema.json
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Expand Up @@ -68,22 +68,24 @@
"type": "object",
"properties": {
"germline_var_keep": {
"type": "array",
"type": "string",
"description": "List of germline variant callers to use. Must include at least one of [deepvariant, clair].",
"items": {
"type": "string",
"enum": ["deepvariant", "clair"]
},
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Copilot AI Apr 30, 2026

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germline_var_keep now allows type: "string", but the allowed values are only constrained via items.enum (which applies only when the value is an array). As a result, any arbitrary string would validate successfully and bypass the intended [deepvariant, clair] restriction. Consider using oneOf/anyOf to separately validate the string form (e.g., enum/pattern) vs the array form, or keep this as an array-only parameter.

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"minItems": 1
"minItems": 1,
"default": "['deepvariant', 'clair']"
},
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germline_var_keep is typed as an array, but the schema default is currently a string (and not valid JSON). This will break downstream tooling that reads defaults from the schema. Set default to a JSON array (e.g., ["deepvariant","clair"]) instead of a quoted string.

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germline_var_keep is used throughout the pipeline as a Groovy List (e.g., .contains(), .size(), and comparisons to ['clair'] / ['deepvariant']). Changing the schema type to string (and setting a string default like "['deepvariant', 'clair']") will encourage invalid user input and can break runtime logic; it also makes the schema invalid because items/minItems apply to arrays, not strings. Please revert this property to type: "array" with items.type: "string", keep minItems, and use a real JSON array for default (e.g. ["deepvariant","clair"]).

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"somatic_var_keep": {
"type": "array",
"type": "string",
"description": "List of somatic variant callers to use. Must include at least one of [deepsomatic, clair].",
"items": {
"type": "string",
"enum": ["deepsomatic", "clair"]
},
"minItems": 1
"minItems": 1,
"default": "['deepsomatic', 'clair']"
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somatic_var_keep is typed as an array, but the schema default is currently a string (and not valid JSON). This will confuse validation/docs generation that expects an array default. Change default to a JSON array (e.g., ["deepsomatic","clair"]).

Suggested change
"default": "['deepsomatic', 'clair']"
"default": ["deepsomatic", "clair"]

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Same issue for somatic_var_keep: the workflow expects a List (uses .contains() / .size() patterns), but the schema now declares it as string with items/minItems and a stringified list default. This makes the schema inconsistent/invalid and can lead to runtime misbehavior if users supply a string. Please keep it as type: "array" with an enum-constrained items, and set default to a JSON array like ["deepsomatic","clair"].

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},
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germline_var_keep and somatic_var_keep are typed as arrays, but their default values are currently JSON strings (e.g. "['deepvariant', 'clair']"). In JSON Schema, default should match the declared type; this will break schema validation / generated docs. Set these defaults to actual JSON arrays (e.g. ["deepvariant", "clair"]).

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"germline_var_combine": {
"type": "string",
Expand Down Expand Up @@ -111,6 +113,18 @@
}
}
},
"longphase_options": {
"title": "Longphase options",
"type": "object",
"description": "Options for Longphase phasing of small variants",
"properties": {
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longphase_options is added under $defs, but it isn't referenced in the top-level allOf list. As a result, longphase_tag_supplementary defined there won't be part of the effective schema grouping/metadata. Add a $ref to #/$defs/longphase_options in allOf (and avoid duplicating the param elsewhere) so it shows up correctly in the schema-driven UI/docs.

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"longphase_tag_supplementary": {
"type": "boolean",
"description": "Whether to include supplementary alignments in Longphase haplotype tagging.",
"default": false
}
}
},
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PR title/description indicate this is only about adding a Longphase supplementary-alignment haplotag option, but this PR also changes schema defaults for *_var_keep, adds new schema properties for generate_gvcf / skip_modkit, and updates the documented default for severus_minsupport. Please update the PR description (or split into separate PRs) so reviewers understand the full scope and rationale for these additional changes.

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"reference_genome_options": {
"title": "Reference genome options",
"type": "object",
Expand All @@ -126,7 +140,6 @@
},
"igenomes_ignore": {
"type": "boolean",
"default": false,
"description": "Do not load the iGenomes reference config.",
"fa_icon": "fas fa-ban",
"hidden": true,
Expand Down Expand Up @@ -202,7 +215,6 @@
},
"download_vep_cache": {
"type": "boolean",
"default": false,
"description": "Download the VEP cache if not already present"
},
"vep_custom": {
Expand Down Expand Up @@ -283,7 +295,6 @@
},
"ascat_pdf_plots": {
"type": "boolean",
"default": false,
"description": "Boolean for ASCAT production of pdf plots (entered as string)"
}
}
Expand All @@ -307,72 +318,58 @@
"properties": {
"skip_qc": {
"type": "boolean",
"default": false,
"description": "Skips all QC steps"
},
"skip_cramino": {
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A number of boolean parameters had their default: false removed from the schema (e.g. all skip_* flags, use_gpu, plus others elsewhere like igenomes_ignore, download_vep_cache, ascat_pdf_plots, and generic help/version flags). Even though JSON Schema default is informational, nf-core tooling/docs and UI generation typically rely on it to display correct defaults and keep the schema aligned with nextflow.config. Please restore the default values (at least for the params that are explicitly defaulted in nextflow.config).

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"type": "boolean",
"default": false,
"description": "Skips Cramino"
},
"skip_mosdepth": {
"type": "boolean",
"default": false,
"description": "Skips Mosdepth"
},
"skip_bamstats": {
"type": "boolean",
"default": false,
"description": "Skips samtools flagstat, stats, and idxstats"
},
"skip_wakhan": {
"type": "boolean",
"default": false,
"description": "Skips wakhan"
},
"skip_fiber": {
"type": "boolean",
"default": false,
"description": "Skip Fibertools steps"
},
"skip_ascat": {
"type": "boolean",
"default": false,
"description": "Skip ASCAT"
},
"skip_m6a": {
"type": "boolean",
"default": false,
"description": "Skip m6a calling by Fibertools"
},
"skip_vep": {
"type": "boolean",
"default": false,
"description": "Skip VEP annotation"
},
"skip_normalfiber": {
"type": "boolean",
"default": false,
"description": "Skip Fibertools steps for the normal sample"
},
"skip_nanoplot": {
"type": "boolean",
"default": false,
"description": "Skip Nanoplot"
},
"skip_whatshapstats": {
"type": "boolean",
"default": false,
"description": "Skip WhatsHap stats"
},
"skip_modcall": {
"type": "boolean",
"default": false,
"description": "Skip modification calling"
},
"use_gpu": {
"type": "boolean",
"default": false,
"description": "Use GPU for supported tools (e.g. DeepVariant, DeepSomatic, Clair3)"
}
}
Expand Down Expand Up @@ -434,7 +431,6 @@
"properties": {
"version": {
"type": "boolean",
"default": false,
"description": "Display version and exit.",
"fa_icon": "fas fa-question-circle",
"hidden": true
Expand All @@ -458,7 +454,6 @@
},
"plaintext_email": {
"type": "boolean",
"default": false,
"description": "Send plain-text email instead of HTML.",
"fa_icon": "fas fa-remove-format",
"hidden": true
Expand All @@ -473,7 +468,6 @@
},
"monochrome_logs": {
"type": "boolean",
"default": false,
"description": "Do not use coloured log outputs.",
"fa_icon": "fas fa-palette",
"hidden": true
Expand Down Expand Up @@ -525,17 +519,14 @@
},
"help": {
"type": "boolean",
"default": false,
"description": "Display the help message."
},
"help_full": {
"type": "boolean",
"default": false,
"description": "Display the full detailed help message."
},
"show_hidden": {
"type": "boolean",
"default": false,
"description": "Display hidden parameters in the help message (only works when --help or --help_full are provided)."
}
}
Expand All @@ -551,6 +542,9 @@
{
"$ref": "#/$defs/small_variant_calling_options"
},
{
"$ref": "#/$defs/longphase_options"
},
{
"$ref": "#/$defs/reference_genome_options"
},
Expand Down Expand Up @@ -581,5 +575,13 @@
{
"$ref": "#/$defs/generic_options"
}
]
],
"properties": {
"generate_gvcf": {
"type": "boolean"
},
Comment on lines +580 to +582
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Top-level properties.generate_gvcf is missing a description/help_text/default and is not grouped with the other small variant calling options in $defs. This makes the schema inconsistent and may cause nf-core schema docs / UI grouping to omit or misplace the parameter metadata.

Suggested change
"generate_gvcf": {
"type": "boolean"
},

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"skip_modkit": {
"type": "boolean"
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Top-level properties.skip_modkit is defined without description/help_text/default and outside the existing skip_options group. To keep schema validation + rendered docs consistent, this should be defined alongside the other skip parameters (with matching metadata) rather than as a bare root property.

Suggested change
},
"skip_modkit": {
"type": "boolean"

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}
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The new top-level properties block defines generate_gvcf, longphase_tag_supplementary, and skip_modkit with only type, dropping their descriptions/defaults and bypassing the existing $defs grouping pattern used elsewhere in this schema. Instead, define these parameters in the appropriate $defs sections (e.g., generate_gvcf in small-variant options, skip_modkit in skip options, longphase_tag_supplementary in longphase options) and reference those groups from allOf, removing this partial top-level properties block.

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}
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The new top-level properties entries for generate_gvcf and skip_modkit are incomplete (no description/default) and also bypass the existing parameter grouping via $defs/allOf (e.g. skip_modkit should live under #/$defs/skip_options). This will make schema-generated docs/UI inconsistent with docs/usage.md and other params. Consider moving these definitions into the appropriate $defs sections and adding description (and default if the schema is intended to carry defaults).

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}
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