From c14136ddcb0494b50486848b661523000d15c644 Mon Sep 17 00:00:00 2001 From: Amber Verhasselt Date: Wed, 29 Apr 2026 13:14:13 +0200 Subject: [PATCH 1/7] add long_phase supplementary alignment tag --- conf/modules.config | 5 ++++ docs/usage.md | 8 ++++++- nextflow.config | 3 +++ nextflow_schema.json | 54 +++++++++++++++++++++++--------------------- 4 files changed, 43 insertions(+), 27 deletions(-) diff --git a/conf/modules.config b/conf/modules.config index 25de8b9..6bd573f 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -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, diff --git a/docs/usage.md b/docs/usage.md index a644732..e7944b3 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -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 | @@ -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 diff --git a/nextflow.config b/nextflow.config index 84c9f48..c0dbb53 100644 --- a/nextflow.config +++ b/nextflow.config @@ -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 diff --git a/nextflow_schema.json b/nextflow_schema.json index a7cc149..7792bcd 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -74,7 +74,8 @@ "type": "string", "enum": ["deepvariant", "clair"] }, - "minItems": 1 + "minItems": 1, + "default": "['deepvariant', 'clair']" }, "somatic_var_keep": { "type": "array", @@ -83,7 +84,8 @@ "type": "string", "enum": ["deepsomatic", "clair"] }, - "minItems": 1 + "minItems": 1, + "default": "['deepsomatic', 'clair']" }, "germline_var_combine": { "type": "string", @@ -111,6 +113,18 @@ } } }, + "longphase_options": { + "title": "Longphase options", + "type": "object", + "description": "Options for Longphase phasing of small variants", + "properties": { + "longphase_tag_supplementary": { + "type": "boolean", + "description": "Whether to include supplementary alignments in Longphase haplotype tagging.", + "default": false + } + } + }, "reference_genome_options": { "title": "Reference genome options", "type": "object", @@ -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, @@ -202,7 +215,6 @@ }, "download_vep_cache": { "type": "boolean", - "default": false, "description": "Download the VEP cache if not already present" }, "vep_custom": { @@ -283,7 +295,6 @@ }, "ascat_pdf_plots": { "type": "boolean", - "default": false, "description": "Boolean for ASCAT production of pdf plots (entered as string)" } } @@ -307,72 +318,58 @@ "properties": { "skip_qc": { "type": "boolean", - "default": false, "description": "Skips all QC steps" }, "skip_cramino": { "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)" } } @@ -434,7 +431,6 @@ "properties": { "version": { "type": "boolean", - "default": false, "description": "Display version and exit.", "fa_icon": "fas fa-question-circle", "hidden": true @@ -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 @@ -473,7 +468,6 @@ }, "monochrome_logs": { "type": "boolean", - "default": false, "description": "Do not use coloured log outputs.", "fa_icon": "fas fa-palette", "hidden": true @@ -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)." } } @@ -581,5 +572,16 @@ { "$ref": "#/$defs/generic_options" } - ] + ], + "properties": { + "generate_gvcf": { + "type": "boolean" + }, + "longphase_tag_supplementary": { + "type": "boolean" + }, + "skip_modkit": { + "type": "boolean" + } + } } From 14b14c7dd86fa47198f8e123dc02a0516d72aa32 Mon Sep 17 00:00:00 2001 From: Amber Verhasselt Date: Wed, 29 Apr 2026 15:23:47 +0200 Subject: [PATCH 2/7] fix schema --- nextflow_schema.json | 3 +++ 1 file changed, 3 insertions(+) diff --git a/nextflow_schema.json b/nextflow_schema.json index 7792bcd..77c24c2 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -542,6 +542,9 @@ { "$ref": "#/$defs/small_variant_calling_options" }, + { + "$ref": "#/$defs/longphase_options" + }, { "$ref": "#/$defs/reference_genome_options" }, From c0e3ab26f33a3d3e57aebfddf4c7f03d5dd49337 Mon Sep 17 00:00:00 2001 From: Amber Verhasselt Date: Wed, 29 Apr 2026 15:34:18 +0200 Subject: [PATCH 3/7] fix schema 2.0 --- nextflow_schema.json | 3 --- 1 file changed, 3 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 77c24c2..7da44c9 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -580,9 +580,6 @@ "generate_gvcf": { "type": "boolean" }, - "longphase_tag_supplementary": { - "type": "boolean" - }, "skip_modkit": { "type": "boolean" } From af57f2091d61dfe7b362f8d1a854a7f3efa27370 Mon Sep 17 00:00:00 2001 From: Amber Verhasselt Date: Wed, 29 Apr 2026 15:59:38 +0200 Subject: [PATCH 4/7] fix schema 3.0 --- nextflow_schema.json | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 7da44c9..8830e96 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -65,10 +65,10 @@ }, "small_variant_calling_options": { "title": "options for small variant calling", - "type": "object", + "type": "string", "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", @@ -78,7 +78,7 @@ "default": "['deepvariant', 'clair']" }, "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", From f4e7cc08958abdacd8b06567a53788215ba7c948 Mon Sep 17 00:00:00 2001 From: Amber Verhasselt Date: Wed, 29 Apr 2026 16:06:00 +0200 Subject: [PATCH 5/7] fix schema 4.0 --- nextflow_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 8830e96..d86c2d1 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -65,7 +65,7 @@ }, "small_variant_calling_options": { "title": "options for small variant calling", - "type": "string", + "type": "object", "properties": { "germline_var_keep": { "type": "string", From bb3199d28cb1080909c54f6639ced2f8244164bb Mon Sep 17 00:00:00 2001 From: Amber Verhasselt Date: Wed, 29 Apr 2026 16:14:31 +0200 Subject: [PATCH 6/7] fix schema 5.0 --- nextflow_schema.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index d86c2d1..202b11f 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -68,24 +68,24 @@ "type": "object", "properties": { "germline_var_keep": { - "type": "string", + "type": "array", "description": "List of germline variant callers to use. Must include at least one of [deepvariant, clair].", "items": { "type": "string", "enum": ["deepvariant", "clair"] }, "minItems": 1, - "default": "['deepvariant', 'clair']" + "default": ["deepvariant", "clair"] }, "somatic_var_keep": { - "type": "string", + "type": "array", "description": "List of somatic variant callers to use. Must include at least one of [deepsomatic, clair].", "items": { "type": "string", "enum": ["deepsomatic", "clair"] }, "minItems": 1, - "default": "['deepsomatic', 'clair']" + "default": ["deepsomatic", "clair"] }, "germline_var_combine": { "type": "string", From be64ce509d6b757809ec2e30aca79253907dac0a Mon Sep 17 00:00:00 2001 From: Amber Verhasselt Date: Thu, 30 Apr 2026 07:32:15 +0200 Subject: [PATCH 7/7] fix schema 6.0 --- nextflow_schema.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index 202b11f..ae16d4c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -68,24 +68,24 @@ "type": "object", "properties": { "germline_var_keep": { - "type": "array", + "type": ["string", "array"], "description": "List of germline variant callers to use. Must include at least one of [deepvariant, clair].", "items": { "type": "string", "enum": ["deepvariant", "clair"] }, "minItems": 1, - "default": ["deepvariant", "clair"] + "default": "['deepvariant', 'clair']" }, "somatic_var_keep": { - "type": "array", + "type": ["string", "array"], "description": "List of somatic variant callers to use. Must include at least one of [deepsomatic, clair].", "items": { "type": "string", "enum": ["deepsomatic", "clair"] }, "minItems": 1, - "default": ["deepsomatic", "clair"] + "default": "['deepsomatic', 'clair']" }, "germline_var_combine": { "type": "string",