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Severus min support param and skip_fibernormal #143

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Severus min support param and skip_fibernormal #143

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cf57965
add options to specify min support severus
ljwharbers Mar 12, 2026
d303521
change to skip_fibernormal
ljwharbers Mar 12, 2026
457e869
Update conf/modules.config
ljwharbers Mar 12, 2026
43f9481
Update nextflow.config
ljwharbers Mar 12, 2026
2b7bd98
update snaps
ljwharbers Mar 12, 2026
266ec75
Merge branch 'dev' into severus_fiber_params
robert-a-forsyth Mar 13, 2026
e5fe4be
dev merge
ljwharbers Mar 13, 2026
89edfc7
pull conflict
ljwharbers Mar 13, 2026
b2ebc8e
Merge branch 'dev' into severus_fiber_params
ljwharbers Mar 13, 2026
7077cd9
snapshot update, schema fix
ljwharbers Mar 13, 2026
7f80cd1
Merge branch 'dev' into severus_fiber_params
robert-a-forsyth Mar 17, 2026
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2 changes: 1 addition & 1 deletion conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -248,7 +248,7 @@ process {

withName: '.*:SEVERUS' {
ext.prefix = "."
ext.args = '--min-support 3 --output-read-ids '
ext.args = { "--min-support ${params.severus_minsupport} --output-read-ids " }
publishDir = [
path: { "${params.outdir}/${meta.id}/variants/severus" },
mode: params.publish_dir_mode,
Expand Down
9 changes: 5 additions & 4 deletions nextflow.config
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Expand Up @@ -26,9 +26,6 @@ params {
vep_custom = null
vep_custom_tbi = null


normal_fiber = true

// Skip options
skip_qc = false
skip_cramino = false
Expand All @@ -38,6 +35,7 @@ params {
skip_ascat = false
skip_wakhan = false
skip_fiber = false
skip_normalfiber = false
skip_m6a = false
skip_vep = false
skip_whatshapstats = false
Expand All @@ -48,7 +46,10 @@ params {
save_secondary_alignment = true

// Fibertools options
params.autocorrelation = null
autocorrelation = null

// Severus options
severus_minsupport = 3

// ASCAT options
ascat_ploidy = null
Expand Down
113 changes: 89 additions & 24 deletions nextflow_schema.json
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Expand Up @@ -70,23 +70,6 @@
"fa_icon": "fas fa-ban",
"hidden": true,
"default": "s3://ngi-igenomes/igenomes/"
},
"vep_cache": {
"type": "string",
"description": "Path to VEP cache directory.",
"fa_icon": "fas fa-database",
"help_text": "Path to the directory containing the VEP cache. If you are using an iGenomes reference, this will be set automatically. Otherwise, you will need to provide this path yourself."
},
"vep_cache_version": {
"type": "integer",
"description": "Version of the VEP cache to use.",
"fa_icon": "fas fa-hashtag",
"help_text": "The version of the VEP cache to use. This should match the version of VEP being used."
},
"vep_args": {
"type": "string",
"description": "Additional command line arguments to pass to VEP.",
"fa_icon": "fas fa-terminal"
}
}
},
Expand All @@ -111,6 +94,66 @@
}
}
},
"fibertools_options": {
"title": "Fibertools options",
"type": "object",
"description": "",
"default": "",
"properties": {
"autocorrelation": {
"type": "string"
}
}
},
"vep_options": {
"title": "VEP options",
"type": "object",
"description": "",
"default": "",
"properties": {
"vep_cache": {
"type": "string",
"description": "Path to VEP cache directory.",
"fa_icon": "fas fa-database",
"help_text": "Path to the directory containing the VEP cache. If you are using an iGenomes reference, this will be set automatically. Otherwise, you will need to provide this path yourself.",
"default": "s3://annotation-cache/vep_cache/"
},
"vep_args": {
"type": "string",
"description": "Additional command line arguments to pass to VEP.",
"fa_icon": "fas fa-terminal",
"default": "--everything --filter_common --per_gene --total_length --offline --format vcf"
},
"vep_cache_version": {
"type": "integer",
"description": "Version of the VEP cache to use.",
"fa_icon": "fas fa-hashtag",
"help_text": "The version of the VEP cache to use. This should match the version of VEP being used.",
"default": 113
},
"download_vep_cache": {
"type": "boolean"
},
"vep_custom": {
"type": "string"
},
"vep_custom_tbi": {
"type": "string"
}
}
},
"severus_options": {
"title": "Severus options",
"type": "object",
"description": "",
"default": "",
"properties": {
"severus_minsupport": {
"type": "integer",
"default": 3
}
}
},
"ascat_parameters": {
"title": "ASCAT parameters",
"type": "object",
Expand Down Expand Up @@ -173,6 +216,17 @@
}
}
},
"wakhan_options": {
"title": "Wakhan options",
"type": "object",
"description": "",
"default": "",
"properties": {
"wakhan_chroms": {
"type": "string"
}
}
},
"skip_options": {
"title": "Skip options",
"type": "object",
Expand Down Expand Up @@ -211,6 +265,12 @@
"type": "boolean",
"description": "Skip m6a calling by Fibertools"
},
"skip_vep": {
"type": "boolean"
},
"skip_normalfiber": {
"type": "boolean"
},
"skip_nanoplot": {
"type": "boolean",
"description": "Skip Nanoplot"
Expand Down Expand Up @@ -364,13 +424,6 @@
"description": "Suffix to add to the trace report filename. Default is the date and time in the format yyyy-MM-dd_HH-mm-ss.",
"hidden": true
},
"normal_fiber": {
"type": "boolean",
"default": true,
"description": "do fiber-seq on normal samples",
"fa_icon": "fas fa-fiber",
"hidden": true
},
"help": {
"type": ["boolean", "string"],
"description": "Display the help message."
Expand All @@ -396,9 +449,21 @@
{
"$ref": "#/$defs/minimap2_options"
},
{
"$ref": "#/$defs/fibertools_options"
},
{
"$ref": "#/$defs/vep_options"
},
{
"$ref": "#/$defs/severus_options"
},
{
"$ref": "#/$defs/ascat_parameters"
},
{
"$ref": "#/$defs/wakhan_options"
},
{
"$ref": "#/$defs/skip_options"
},
Expand Down
2 changes: 1 addition & 1 deletion tests/default.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -508,7 +508,7 @@
"read_qual.txt:md5,b918430d35354dad1d7f02f21e4cd4ed"
]
],
"timestamp": "2026-03-13T17:15:05.714239372",
"timestamp": "2026-03-13T15:33:42.343920246",
"meta": {
"nf-test": "0.9.4",
"nextflow": "25.10.0"
Expand Down
12 changes: 6 additions & 6 deletions workflows/lrsomatic.nf
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Expand Up @@ -257,7 +257,10 @@ workflow LRSOMATIC {
// predict m6a in unaligned bam

if (!params.skip_fiber) {
if(!params.normal_fiber){
if (!params.skip_normalfiber){
ubams = ch_cat_ubams
}
else {
ch_cat_ubams
.branch { meta, _bams ->
normal: meta.type == "normal"
Expand All @@ -267,9 +270,6 @@ workflow LRSOMATIC {

normal_bams = ch_cat_ubams_normal_branching.normal
ubams = ch_cat_ubams_normal_branching.tumor
}
else {
ubams = ch_cat_ubams
}
ubams
.branch{ meta, _bams ->
Expand Down Expand Up @@ -329,15 +329,15 @@ workflow LRSOMATIC {
FIBERTOOLSRS_NUCLEOSOMES.out.bam
)

if(!params.normal_fiber){
if (!params.skip_normalfiber){
fiber_branch.nonFiber
.mix(normal_bams)
.mix(FIBERTOOLSRS_FIRE.out.bam)
.set{ch_cat_ubams}

}
else {
fiber_branch.nonFiber
.mix(normal_bams)
.mix(FIBERTOOLSRS_FIRE.out.bam)
.set{ch_cat_ubams}

Expand Down
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