diff --git a/conf/modules.config b/conf/modules.config index 97493a5..76685f9 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -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, diff --git a/nextflow.config b/nextflow.config index bed1fe4..2dfa72e 100644 --- a/nextflow.config +++ b/nextflow.config @@ -26,9 +26,6 @@ params { vep_custom = null vep_custom_tbi = null - - normal_fiber = true - // Skip options skip_qc = false skip_cramino = false @@ -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 @@ -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 diff --git a/nextflow_schema.json b/nextflow_schema.json index b68ffd1..beb2b8c 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -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" } } }, @@ -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", @@ -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", @@ -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" @@ -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." @@ -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" }, diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 8a214ec..17d3996 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -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" diff --git a/workflows/lrsomatic.nf b/workflows/lrsomatic.nf index e34b636..bc0f4c9 100644 --- a/workflows/lrsomatic.nf +++ b/workflows/lrsomatic.nf @@ -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" @@ -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 -> @@ -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}