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Add an option to pass extra resources to vcfanno #588

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merged 9 commits into from
Aug 9, 2024
Merged

Add an option to pass extra resources to vcfanno #588

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9542a38
add extra resource
ramprasadn Aug 8, 2024
7f3e648
update changelog
ramprasadn Aug 9, 2024
c8c71ed
Merge branch 'dev' into dynamic-anno-res
ramprasadn Aug 9, 2024
05707c0
Update nextflow_schema.json
ramprasadn Aug 9, 2024
d1894b5
Update annotate_mt_snvs.nf
ramprasadn Aug 9, 2024
5bd184a
Update prepare_references.nf
ramprasadn Aug 9, 2024
6bbc927
Update annotate_genome_snvs.nf
ramprasadn Aug 9, 2024
99805a4
Update prepare_references.nf
ramprasadn Aug 9, 2024
08302de
Update prepare_references.nf
ramprasadn Aug 9, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Added`

- A new parameter `vcfanno_extra_resources` to pass an extra resource to vcfanno [#588](https://github.com/nf-core/raredisease/pull/588)
- A new parameter `scatter_count` to control how many interval files are created from a genome (used to parallelize annotations) [#585](https://github.com/nf-core/raredisease/pull/585)
- Print warning messages if user intends to perform ranking when there are no affected samples [#579](https://github.com/nf-core/raredisease/pull/579)
- Two new parameters `skip_repeat_annotation` and `skip_repeat_calling` to skip calling and annotation of repeat expansions [#574](https://github.com/nf-core/raredisease/pull/574)
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1 change: 1 addition & 0 deletions main.nf
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Expand Up @@ -58,6 +58,7 @@ params.variant_consequences_sv = getGenomeAttribute('variant_consequence
params.vep_filters = getGenomeAttribute('vep_filters')
params.vep_filters_scout_fmt = getGenomeAttribute('vep_filters_scout_fmt')
params.vcf2cytosure_blacklist = getGenomeAttribute('vcf2cytosure_blacklist')
params.vcfanno_extra_resources = getGenomeAttribute('vcfanno_extra_resources')
params.vcfanno_resources = getGenomeAttribute('vcfanno_resources')
params.vcfanno_toml = getGenomeAttribute('vcfanno_toml')
params.vcfanno_lua = getGenomeAttribute('vcfanno_lua')
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8 changes: 8 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -402,6 +402,14 @@
"fa_icon": "fas fa-file",
"description": "Path to vcf2cytosure blacklist file"
},
"vcfanno_extra_resources": {
"type": "string",
"exists": true,
"format": "file-path",
"description": "Path to a VCF file containing annotations.",
"help_text": "can be used to supply case-specific annotations in addition to those provided using --vcfanno_resources",
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"fa_icon": "fas fa-file"
},
"vcfanno_resources": {
"type": "string",
"exists": true,
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5 changes: 3 additions & 2 deletions subworkflows/local/annotate_genome_snvs.nf
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Expand Up @@ -28,7 +28,8 @@ workflow ANNOTATE_GENOME_SNVS {
analysis_type // string: [mandatory] 'wgs' or 'wes'
ch_cadd_header // channel: [mandatory] [ path(txt) ]
ch_cadd_resources // channel: [mandatory] [ path(annotation) ]
ch_vcfanno_resources // channel: [mandatory] [ path(resources) ]
ch_vcfanno_extra // channel: [mandatory] [ path(resources & indices) ]
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Suggested change
ch_vcfanno_extra // channel: [mandatory] [ path(resources & indices) ]
ch_vcfanno_extra // channel: [mandatory] [ path(vcf), path(tbi) ]

?

ch_vcfanno_resources // channel: [mandatory] [ path(resources & indices) ]
ch_vcfanno_lua // channel: [mandatory] [ path(lua) ]
ch_vcfanno_toml // channel: [mandatory] [ path(toml) ]
val_vep_genome // string: [mandatory] GRCh37 or GRCh38
Expand Down Expand Up @@ -69,7 +70,7 @@ workflow ANNOTATE_GENOME_SNVS {

GATK4_SELECTVARIANTS.out.vcf
.join(GATK4_SELECTVARIANTS.out.tbi)
.map { meta, vcf, tbi -> return [meta, vcf, tbi, []] }
.combine(ch_vcfanno_extra)
.set { ch_vcfanno_in }

VCFANNO (ch_vcfanno_in, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources)
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9 changes: 6 additions & 3 deletions subworkflows/local/annotate_mt_snvs.nf
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Expand Up @@ -19,8 +19,9 @@ workflow ANNOTATE_MT_SNVS {
ch_cadd_header // channel: [mandatory] [ path(txt) ]
ch_cadd_resources // channel: [mandatory] [ path(annotation) ]
ch_genome_fasta // channel: [mandatory] [ val(meta), path(fasta) ]
ch_vcfanno_lua // channel: [mandatory] [ path(lua) ]
ch_vcfanno_resources // channel: [mandatory] [ path(resources) ]
ch_vcfanno_extra // channel: [mandatory] [ path(resources & indices) ]
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Suggested change
ch_vcfanno_extra // channel: [mandatory] [ path(resources & indices) ]
ch_vcfanno_extra // channel: [mandatory] [ path(vcf), path(tbi) ]

Shouldn't it be something like this?

ch_vcfanno_lua // channel: [mandatory] [ path(lua) ]
ch_vcfanno_resources // channel: [mandatory] [ path(resources & indices) ]
ch_vcfanno_toml // channel: [mandatory] [ path(toml) ]
val_vep_genome // string: [mandatory] GRCh37 or GRCh38
val_vep_cache_version // string: [mandatory] 107
Expand All @@ -45,7 +46,9 @@ workflow ANNOTATE_MT_SNVS {

// Vcfanno
ZIP_TABIX_HMTNOTE_MT.out.gz_tbi
.map { meta, vcf, tbi -> return [meta + [prefix: meta.prefix + "_vcfanno"], vcf, tbi, []]}
.combine(ch_vcfanno_extra)
.map { meta, vcf, tbi, resources -> return [meta + [prefix: meta.prefix + "_vcfanno"], vcf, tbi, resources]}
.dump (tag:'test')
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.set { ch_in_vcfanno }

VCFANNO_MT(ch_in_vcfanno, ch_vcfanno_toml, ch_vcfanno_lua, ch_vcfanno_resources)
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19 changes: 14 additions & 5 deletions subworkflows/local/prepare_references.nf
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Expand Up @@ -22,6 +22,7 @@ include { SAMTOOLS_FAIDX as SAMTOOLS_FAIDX_MT_SHIFT } from '../../modul
include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_GENOME } from '../../modules/nf-core/sentieon/bwaindex/main'
include { SENTIEON_BWAINDEX as SENTIEON_BWAINDEX_MT_SHIFT } from '../../modules/nf-core/sentieon/bwaindex/main'
include { TABIX_BGZIPTABIX as TABIX_PBT } from '../../modules/nf-core/tabix/bgziptabix/main'
include { TABIX_BGZIPTABIX as TABIX_VCFANNOEXTRA } from '../../modules/nf-core/tabix/bgziptabix/main'
include { TABIX_TABIX as TABIX_DBSNP } from '../../modules/nf-core/tabix/tabix/main'
include { TABIX_TABIX as TABIX_GNOMAD_AF } from '../../modules/nf-core/tabix/tabix/main'
include { TABIX_TABIX as TABIX_PT } from '../../modules/nf-core/tabix/tabix/main'
Expand All @@ -36,14 +37,16 @@ workflow PREPARE_REFERENCES {
ch_gnomad_af_tab // channel: [optional; used in for snv annotation] [ val(meta), path(tab) ]
ch_known_dbsnp // channel: [optional; used only by sentieon] [ val(meta), path(vcf) ]
ch_target_bed // channel: [mandatory for WES] [ path(bed) ]
ch_vcfanno_extra_unprocessed // channel: [mandatory] [ val(meta), path(vcf) ]
ch_vep_cache // channel: [mandatory for annotation] [ path(cache) ]

main:
ch_versions = Channel.empty()
ch_tbi = Channel.empty()
ch_bgzip_tbi = Channel.empty()
ch_bwa = Channel.empty()
ch_sentieonbwa = Channel.empty()
ch_versions = Channel.empty()
ch_tbi = Channel.empty()
ch_bgzip_tbi = Channel.empty()
ch_bwa = Channel.empty()
ch_sentieonbwa = Channel.empty()
ch_vcfanno_extra = Channel.empty()

// Genome indices
SAMTOOLS_FAIDX_GENOME(ch_genome_fasta, [[],[]])
Expand Down Expand Up @@ -87,6 +90,10 @@ workflow PREPARE_REFERENCES {
TABIX_GNOMAD_AF(ch_gnomad_af_tab)
TABIX_PT(ch_target_bed).tbi.set { ch_tbi }
TABIX_PBT(ch_target_bed).gz_tbi.set { ch_bgzip_tbi }
TABIX_VCFANNOEXTRA(ch_vcfanno_extra_unprocessed)
.gz_tbi
.map { meta, vcf, tbi -> return [[vcf,tbi]] }
.set {ch_vcfanno_extra}

// Generate bait and target intervals
GATK_BILT(ch_target_bed, ch_dict).interval_list
Expand Down Expand Up @@ -125,6 +132,7 @@ workflow PREPARE_REFERENCES {
ch_versions = ch_versions.mix(TABIX_GNOMAD_AF.out.versions)
ch_versions = ch_versions.mix(TABIX_PT.out.versions)
ch_versions = ch_versions.mix(TABIX_PBT.out.versions)
ch_versions = ch_versions.mix(TABIX_VCFANNOEXTRA.out.versions)
ch_versions = ch_versions.mix(TABIX_DBSNP.out.versions)
ch_versions = ch_versions.mix(GATK_BILT.out.versions)
ch_versions = ch_versions.mix(GATK_ILT.out.versions)
Expand Down Expand Up @@ -153,6 +161,7 @@ workflow PREPARE_REFERENCES {
gnomad_af_idx = TABIX_GNOMAD_AF.out.tbi.collect() // channel: [ val(meta), path(fasta) ]
known_dbsnp_tbi = TABIX_DBSNP.out.tbi.collect() // channel: [ val(meta), path(fasta) ]
target_bed = Channel.empty().mix(ch_tbi, ch_bgzip_tbi).collect() // channel: [ val(meta), path(bed), path(tbi) ]
vcfanno_extra = ch_vcfanno_extra.ifEmpty([[]]) // channel: [ path(intervals) ]
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bait_intervals = CAT_CAT_BAIT.out.file_out.map{ meta, inter -> inter}.collect() // channel: [ path(intervals) ]
target_intervals = GATK_BILT.out.interval_list.map{ meta, inter -> inter}.collect() // channel: [ path(interval_list) ]
vep_resources = UNTAR_VEP_CACHE.out.untar.map{meta, files -> [files]}.collect() // channel: [ path(cache) ]
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36 changes: 21 additions & 15 deletions workflows/raredisease.nf
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Expand Up @@ -188,21 +188,23 @@ workflow RAREDISEASE {
//
// Initialize file channels for PREPARE_REFERENCES subworkflow
//
ch_genome_fasta = Channel.fromPath(params.fasta).map { it -> [[id:it[0].simpleName], it] }.collect()
ch_genome_fai = params.fai ? Channel.fromPath(params.fai).map {it -> [[id:it[0].simpleName], it]}.collect()
: Channel.empty()
ch_genome_dictionary = params.sequence_dictionary ? Channel.fromPath(params.sequence_dictionary).map {it -> [[id:it[0].simpleName], it]}.collect()
: Channel.empty()
ch_gnomad_af_tab = params.gnomad_af ? Channel.fromPath(params.gnomad_af).map{ it -> [[id:it[0].simpleName], it] }.collect()
: Channel.value([[],[]])
ch_dbsnp = params.known_dbsnp ? Channel.fromPath(params.known_dbsnp).map{ it -> [[id:it[0].simpleName], it] }.collect()
: Channel.value([[],[]])
ch_mt_fasta = params.mt_fasta ? Channel.fromPath(params.mt_fasta).map { it -> [[id:it[0].simpleName], it] }.collect()
: Channel.empty()
ch_target_bed_unprocessed = params.target_bed ? Channel.fromPath(params.target_bed).map{ it -> [[id:it[0].simpleName], it] }.collect()
: Channel.value([[],[]])
ch_vep_cache_unprocessed = params.vep_cache ? Channel.fromPath(params.vep_cache).map { it -> [[id:'vep_cache'], it] }.collect()
: Channel.value([[],[]])
ch_genome_fasta = Channel.fromPath(params.fasta).map { it -> [[id:it[0].simpleName], it] }.collect()
ch_genome_fai = params.fai ? Channel.fromPath(params.fai).map {it -> [[id:it[0].simpleName], it]}.collect()
: Channel.empty()
ch_genome_dictionary = params.sequence_dictionary ? Channel.fromPath(params.sequence_dictionary).map {it -> [[id:it[0].simpleName], it]}.collect()
: Channel.empty()
ch_gnomad_af_tab = params.gnomad_af ? Channel.fromPath(params.gnomad_af).map{ it -> [[id:it[0].simpleName], it] }.collect()
: Channel.value([[],[]])
ch_dbsnp = params.known_dbsnp ? Channel.fromPath(params.known_dbsnp).map{ it -> [[id:it[0].simpleName], it] }.collect()
: Channel.value([[],[]])
ch_mt_fasta = params.mt_fasta ? Channel.fromPath(params.mt_fasta).map { it -> [[id:it[0].simpleName], it] }.collect()
: Channel.empty()
ch_target_bed_unprocessed = params.target_bed ? Channel.fromPath(params.target_bed).map{ it -> [[id:it[0].simpleName], it] }.collect()
: Channel.value([[],[]])
ch_vcfanno_extra_unprocessed = params.vcfanno_extra_resources ? Channel.fromPath(params.vcfanno_extra_resources).map { it -> [[id:it.baseName], it] }.collect()
: Channel.empty()
ch_vep_cache_unprocessed = params.vep_cache ? Channel.fromPath(params.vep_cache).map { it -> [[id:'vep_cache'], it] }.collect()
: Channel.value([[],[]])

//
// Prepare references and indices.
Expand All @@ -215,6 +217,7 @@ workflow RAREDISEASE {
ch_gnomad_af_tab,
ch_dbsnp,
ch_target_bed_unprocessed,
ch_vcfanno_extra_unprocessed,
ch_vep_cache_unprocessed
)
.set { ch_references }
Expand Down Expand Up @@ -306,6 +309,7 @@ workflow RAREDISEASE {
: Channel.value([])
ch_variant_consequences_sv = params.variant_consequences_sv ? Channel.fromPath(params.variant_consequences_sv).collect()
: Channel.value([])
ch_vcfanno_extra = ch_references.vcfanno_extra
ch_vcfanno_resources = params.vcfanno_resources ? Channel.fromPath(params.vcfanno_resources).splitText().map{it -> it.trim()}.collect()
: Channel.value([])
ch_vcf2cytosure_blacklist = params.vcf2cytosure_blacklist ? Channel.fromPath(params.vcf2cytosure_blacklist).collect()
Expand Down Expand Up @@ -514,6 +518,7 @@ workflow RAREDISEASE {
params.analysis_type,
ch_cadd_header,
ch_cadd_resources,
ch_vcfanno_extra,
ch_vcfanno_resources,
ch_vcfanno_lua,
ch_vcfanno_toml,
Expand Down Expand Up @@ -570,6 +575,7 @@ workflow RAREDISEASE {
ch_cadd_header,
ch_cadd_resources,
ch_genome_fasta,
ch_vcfanno_extra,
ch_vcfanno_lua,
ch_vcfanno_resources,
ch_vcfanno_toml,
Expand Down