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feat: made all steps optional #47

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8f9f413
made process optional
fevac Mar 11, 2026
230c4f5
rename tabix
fevac Mar 11, 2026
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1 change: 1 addition & 0 deletions nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,7 @@ params {
// Temporary inputs
snv_vcf = null
sv_vcf = null
include_process = "snv_local_annotation,snv_filtering,snv_ensemblvep,snv_clinical_filtering,sv_local_annotation,sv_filtering,sv_ensemblvep,sv_clinical_filtering"

// Vep
vep_cache_version = 112
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196 changes: 107 additions & 89 deletions workflows/oncorefiner.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -19,6 +19,7 @@ include { SVDB_QUERY as SVDB_QUERY_DB } from '../modules/nf-core/sv
include { ENSEMBLVEP_VEP as ENSEMBLVEP_SV } from '../modules/nf-core/ensemblvep/vep/main'
include { BCFTOOLS_VIEW as RESEARCH_FILTERING_SV } from '../modules/nf-core/bcftools/view/main'
include { BCFTOOLS_VIEW as CLINICAL_FILTERING_SV } from '../modules/nf-core/bcftools/view/main'
include { TABIX_TABIX as TABIX_SVDB_SV } from '../modules/nf-core/tabix/tabix/main'

//
// MODULE: Local modules
Expand Down Expand Up @@ -72,6 +73,8 @@ workflow ONCOREFINER {
ch_vep_cache = ( params.vep_cache && params.vep_cache.endsWith("tar.gz") ) ? ch_references.vep_resources
: ( params.vep_cache ? channel.fromPath(params.vep_cache).collect() : channel.value([]) )

def include_process = params.include_process ? params.include_process.split(',')*.trim() : []

//
// Read and store paths in the vep_plugin_files file
//
Expand Down Expand Up @@ -100,6 +103,7 @@ workflow ONCOREFINER {
: channel.value([])
ch_vcfanno_extra = params.vcfanno_extra ? channel.fromPath(params.vcfanno_extra).collect()
: []
def resources = ch_vcfanno_extra

// SVDB
ch_sv_dbs = params.svdb_query_dbs ? channel.fromPath(params.svdb_query_dbs)
Expand All @@ -108,125 +112,139 @@ workflow ONCOREFINER {

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
ANNOTATE SNVs
PROCESS SNVs
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
// Process SNV VCF files
if (params.snv_vcf) {

// Vcfanno
ch_snv_vcf
.join(ch_snv_vcf_tbi)
.map { meta, vcf, tbi ->
def resources = ch_vcfanno_extra
tuple(meta, vcf, tbi, resources)
}
.set { ch_vcfanno_in }
VCFANNO (ch_vcfanno_in, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources)
ch_current_snv_vcf = ch_snv_vcf.join(ch_snv_vcf_tbi)

// Vcfanno
if (include_process.contains('snv_local_annotation')) {

VCFANNO (
ch_current_snv_vcf.map { meta, vcf, tbi -> [ meta, vcf, tbi, resources ] },
ch_vcfanno_toml,
ch_vcfanno_lua,
ch_vcfanno_resources
)
ch_current_snv_vcf = VCFANNO.out.vcf
.join(VCFANNO.out.tbi)
}

// Quality Filtering
VCFANNO.out.vcf
.join(VCFANNO.out.tbi)
.map { meta, vcf, tbi ->
tuple(meta, vcf, tbi)
}
.set { ch_research_filtering_in }
RESEARCH_FILTERING(ch_research_filtering_in, [], [], [])
if (include_process.contains('snv_filtering')) {

RESEARCH_FILTERING(ch_current_snv_vcf, [], [], [])

ch_current_snv_vcf = RESEARCH_FILTERING.out.vcf
.join(RESEARCH_FILTERING.out.tbi)
}

// VEP
RESEARCH_FILTERING.out.vcf
.map { meta, vcf ->
def custom_extra_files = params.custom_extra_files ? file(params.custom_extra_files) : []
tuple(meta, vcf, custom_extra_files)
}
.set { ch_vep_snv }

ENSEMBLVEP_SNV (
ch_vep_snv,
params.genome,
"homo_sapiens",
params.vep_cache_version,
ch_vep_cache,
ch_genome_fasta,
ch_vep_extra_files
)
if (include_process.contains('snv_ensemblvep')) {

ENSEMBLVEP_SNV (
ch_current_snv_vcf.map { meta, vcf, tbi -> [ meta, vcf, [] ] },
params.genome,
"homo_sapiens",
params.vep_cache_version,
ch_vep_cache,
ch_genome_fasta,
ch_vep_extra_files
)
ch_current_snv_vcf = ENSEMBLVEP_SNV.out.vcf
.join(ENSEMBLVEP_SNV.out.tbi)
}

// Clinical Filtering
ENSEMBLVEP_SNV.out.vcf
.join(ENSEMBLVEP_SNV.out.tbi)
.map { meta, vcf, tbi ->
tuple(meta, vcf, tbi)
}
.set { ch_clinical_filtering_in }
CLINICAL_FILTERING(ch_clinical_filtering_in, [], [], [])
if (include_process.contains('snv_clinical_filtering')) {

CLINICAL_FILTERING(ch_current_snv_vcf, [], [], [])

ch_current_snv_vcf = CLINICAL_FILTERING.out.vcf
.join(CLINICAL_FILTERING.out.tbi)
}

}

// Process SV VCF files
/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
PROCESS SVs
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
*/
if (params.sv_vcf) {

ch_current_sv_vcf = ch_sv_vcf.join(ch_sv_vcf_tbi)

// SVDB QUERY
ch_sv_dbs
.splitCsv ( header:true )
.multiMap { row ->
vcf_dbs: row.filename
in_frqs: row.in_freq_info_key
in_occs: row.in_allele_count_info_key
out_frqs: row.out_freq_info_key
out_occs: row.out_allele_count_info_key
}
.set { ch_svdb_dbs }

SVDB_QUERY_DB (
ch_sv_vcf,
ch_svdb_dbs.in_occs.toList(),
ch_svdb_dbs.in_frqs.toList(),
ch_svdb_dbs.out_occs.toList(),
ch_svdb_dbs.out_frqs.toList(),
ch_svdb_dbs.vcf_dbs.toList(),
[]
)
if (include_process.contains('sv_local_annotation')) {

ch_sv_dbs
.splitCsv ( header:true )
.multiMap { row ->
vcf_dbs: row.filename
in_frqs: row.in_freq_info_key
in_occs: row.in_allele_count_info_key
out_frqs: row.out_freq_info_key
out_occs: row.out_allele_count_info_key
}
.set { ch_svdb_dbs }

SVDB_QUERY_DB (
ch_current_sv_vcf,
ch_svdb_dbs.in_occs.toList(),
ch_svdb_dbs.in_frqs.toList(),
ch_svdb_dbs.out_occs.toList(),
ch_svdb_dbs.out_frqs.toList(),
ch_svdb_dbs.vcf_dbs.toList(),
[]
)

TABIX_SVDB_SV (
SVDB_QUERY_DB.out.vcf
)
ch_current_sv_vcf = SVDB_QUERY_DB.out.vcf
.join(SVDB_QUERY_DB.out.index)

}

// Quality Filtering
SVDB_QUERY_DB.out.vcf
.map { meta, vcf ->
tuple(meta, vcf, []) }
.set { ch_research_filtering_sv_in }
if (include_process.contains('sv_filtering')) {

RESEARCH_FILTERING_SV(ch_current_sv_vcf, [], [], [])

RESEARCH_FILTERING_SV(ch_research_filtering_sv_in, [], [], [])
ch_current_sv_vcf = RESEARCH_FILTERING_SV.out.vcf
.join(RESEARCH_FILTERING_SV.out.tbi)

}

// VEP
RESEARCH_FILTERING_SV.out.vcf
.map { meta, vcf ->
def custom_extra_files = params.custom_extra_files ? file(params.custom_extra_files) : []
tuple(meta, vcf, custom_extra_files) }
.set { ch_vep_sv }


ENSEMBLVEP_SV(
ch_vep_sv,
params.genome,
"homo_sapiens",
params.vep_cache_version,
ch_vep_cache,
ch_genome_fasta,
ch_vep_extra_files
)
if (include_process.contains('sv_ensemblvep')) {

ENSEMBLVEP_SV(
ch_current_sv_vcf.map { meta, vcf, tbi -> [ meta, vcf, [] ] },
params.genome,
"homo_sapiens",
params.vep_cache_version,
ch_vep_cache,
ch_genome_fasta,
ch_vep_extra_files
)

ch_current_sv_vcf = ENSEMBLVEP_SV.out.vcf
.join(ENSEMBLVEP_SV.out.tbi)
}

// Clinical Filtering
ENSEMBLVEP_SV.out.vcf
.join(ENSEMBLVEP_SV.out.tbi)
.map { meta, vcf, tbi ->
tuple(meta, vcf, tbi)
}
.set { ch_clinical_filtering_sv_in }
CLINICAL_FILTERING_SV(ch_clinical_filtering_sv_in, [], [], [])
if (include_process.contains('sv_clinical_filtering')) {

CLINICAL_FILTERING_SV(ch_current_sv_vcf, [], [], [])

ch_current_sv_vcf = CLINICAL_FILTERING_SV.out.vcf
.join(CLINICAL_FILTERING_SV.out.tbi)
}
}


Expand Down
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