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Add feature to pass vcf.gz files as an additional resource for vcfanno #589

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Aug 12, 2024
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Add feature to pass vcf.gz files as an additional resource for vcfanno #589

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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### `Added`

- A new functionality to pass gzipped resources to vcfanno_extra_resources [#589](https://github.com/nf-core/raredisease/pull/589)
- 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)
Expand Down Expand Up @@ -51,6 +52,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
| | skip_smncopynumbercaller |
| | skip_repeat_annotation |
| | scatter_count |
| | vcfanno_extra_resources |
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Added this one here since I forgot to do so in the previous PR.


## 2.1.0 - Obelix [2024-05-29]

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28 changes: 23 additions & 5 deletions subworkflows/local/prepare_references.nf
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Expand Up @@ -22,7 +22,8 @@ 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_BGZIPTABIX as TABIX_BGZIPINDEX_VCFANNOEXTRA } from '../../modules/nf-core/tabix/bgziptabix/main'
include { TABIX_TABIX as TABIX_VCFANNOEXTRA } from '../../modules/nf-core/tabix/tabix/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 @@ -47,6 +48,8 @@ workflow PREPARE_REFERENCES {
ch_bwa = Channel.empty()
ch_sentieonbwa = Channel.empty()
ch_vcfanno_extra = Channel.empty()
ch_vcfanno_bgzip = Channel.empty()
ch_vcfanno_index = Channel.empty()

// Genome indices
SAMTOOLS_FAIDX_GENOME(ch_genome_fasta, [[],[]])
Expand Down Expand Up @@ -90,12 +93,26 @@ 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
ch_vcfanno_extra_unprocessed
.branch { it ->
bgzipindex: !it[1].toString().endsWith(".gz")
index: it[1].toString().endsWith(".gz")
}
.set { ch_vcfanno_tabix_in }

TABIX_VCFANNOEXTRA(ch_vcfanno_tabix_in.index).tbi
.join(ch_vcfanno_tabix_in.index)
.map { meta, tbi, vcf -> return [[vcf,tbi]]}
.set {ch_vcfanno_index}

TABIX_BGZIPINDEX_VCFANNOEXTRA(ch_vcfanno_tabix_in.bgzipindex).gz_tbi
.map { meta, vcf, tbi -> return [[vcf,tbi]] }
.collect()
.set {ch_vcfanno_extra}
.set {ch_vcfanno_bgzip}

Channel.empty()
.mix(ch_vcfanno_bgzip, ch_vcfanno_index)
.collect()
.set{ch_vcfanno_extra}
// Generate bait and target intervals
GATK_BILT(ch_target_bed, ch_dict).interval_list
GATK_ILT(GATK_BILT.out.interval_list)
Expand Down Expand Up @@ -133,6 +150,7 @@ 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_BGZIPINDEX_VCFANNOEXTRA.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)
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