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Add module bcftools/norm to sarek (in progress) #1483

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Add module bcftools/norm to sarek (in progress) #1483

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4772da1
First modification to contribute to the bcftools/norm module in Sarek
JC-Delmas Apr 25, 2024
451aaec
Changes in the GERMLINE_VCFS_NORM process
JC-Delmas Apr 25, 2024
d97726b
Add fasta argument to POST_VARIANTCALLING process.
JC-Delmas Apr 25, 2024
e034ff0
add fasta input as argument
JC-Delmas Apr 25, 2024
8469832
remove vcfs in the GERMLINE_VCFS_NORM process, replaced by germline_v…
JC-Delmas Apr 25, 2024
e885888
First modification to contribute to the bcftools/norm module in Sarek
JC-Delmas Apr 25, 2024
9e94a05
Changes in the GERMLINE_VCFS_NORM process
JC-Delmas Apr 25, 2024
2bdba7e
Add fasta argument to POST_VARIANTCALLING process.
JC-Delmas Apr 25, 2024
1214f10
add fasta input as argument
JC-Delmas Apr 25, 2024
b7ba4f2
remove vcfs in the GERMLINE_VCFS_NORM process, replaced by germline_v…
JC-Delmas Apr 25, 2024
34bf47b
Update workflows/sarek/main.nf
JC-Delmas Apr 25, 2024
6dff9af
Resolved merge conflict by keeping changes from branch 34bf47baa9d61f…
JC-Delmas Apr 30, 2024
d289261
Refactor normalization and concatenation of VCF files
JC-Delmas Apr 30, 2024
c78af62
Modify and adjust two scripts to add normalization and integrate FAST…
JC-Delmas May 16, 2024
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12 changes: 12 additions & 0 deletions conf/modules/post_variant_calling.config
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,18 @@

process {

withName: 'GERMLINE_VCFS_NORM'{
ext.args = { [
'--multiallelics - both', //split multiallelic sites into biallelic records and both SNPs and indels should be merged separately into two records
'--rm-dup all' //output only the first instance of a record which is present multiple times
].join(' ') }
ext.when = { params.concatenate_vcfs }
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Can we expand this to all vcfs

publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/variant_calling/concat/${meta.id}/" }
]
}

withName: 'GERMLINE_VCFS_CONCAT'{
ext.args = { "-a" }
ext.when = { params.concatenate_vcfs }
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7 changes: 7 additions & 0 deletions modules/nf-core/bcftools/norm/environment.yml
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60 changes: 60 additions & 0 deletions modules/nf-core/bcftools/norm/main.nf
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61 changes: 61 additions & 0 deletions modules/nf-core/bcftools/norm/meta.yml
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3 changes: 2 additions & 1 deletion subworkflows/local/post_variantcalling/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -8,13 +8,14 @@ workflow POST_VARIANTCALLING {

take:
vcfs
fasta
concatenate_vcfs

main:
versions = Channel.empty()

if (concatenate_vcfs){
CONCATENATE_GERMLINE_VCFS(vcfs)
CONCATENATE_GERMLINE_VCFS(vcfs, fasta)

vcfs = vcfs.mix(CONCATENATE_GERMLINE_VCFS.out.vcfs)
versions = versions.mix(CONCATENATE_GERMLINE_VCFS.out.versions)
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41 changes: 29 additions & 12 deletions subworkflows/local/vcf_concatenate_germline/main.nf
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Original file line number Diff line number Diff line change
@@ -1,42 +1,59 @@
//
// CONCATENATE Germline VCFs
//

// Concatenation of germline vcf-files
include { ADD_INFO_TO_VCF } from '../../../modules/local/add_info_to_vcf/main'
include { TABIX_BGZIPTABIX as TABIX_EXT_VCF } from '../../../modules/nf-core/tabix/bgziptabix/main'
include { BCFTOOLS_CONCAT as GERMLINE_VCFS_CONCAT } from '../../../modules/nf-core/bcftools/concat/main'
include { BCFTOOLS_SORT as GERMLINE_VCFS_CONCAT_SORT } from '../../../modules/nf-core/bcftools/sort/main'
include { TABIX_TABIX as TABIX_GERMLINE_VCFS_CONCAT_SORT } from '../../../modules/nf-core/tabix/tabix/main'
include { ADD_INFO_TO_VCF } from '../../../modules/local/add_info_to_vcf/main'
include { TABIX_BGZIPTABIX as TABIX_EXT_VCF } from '../../../modules/nf-core/tabix/bgziptabix/main'
include { BCFTOOLS_NORM as GERMLINE_VCFS_NORM } from '../../../modules/nf-core/bcftools/norm/main'
include { BCFTOOLS_CONCAT as GERMLINE_VCFS_CONCAT } from '../../../modules/nf-core/bcftools/concat/main'
include { BCFTOOLS_SORT as GERMLINE_VCFS_CONCAT_SORT } from '../../../modules/nf-core/bcftools/sort/main'
include { TABIX_TABIX as TABIX_GERMLINE_VCFS_CONCAT_SORT } from '../../../modules/nf-core/tabix/tabix/main'

workflow CONCATENATE_GERMLINE_VCFS {

take:
vcfs
fasta

main:
versions = Channel.empty()

// Concatenate vcf-files
// Add additional information to VCF files
ADD_INFO_TO_VCF(vcfs)

// Compress the VCF files with bgzip
TABIX_EXT_VCF(ADD_INFO_TO_VCF.out.vcf)

// Normalize the VCF files with BCFTOOLS_NORM
GERMLINE_VCFS_NORM(vcf: ADD_INFO_TO_VCF.out.vcf, fasta: fasta)
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I am surprised this runs. Nextflow does not have named inputs

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@FriederikeHanssen I don't think this ran. I fix it here https://github.com/eolaniru/sarek/tree/bcftools-norm_patch and alerted @JC-Delmas as I didn't want to raise a new PR

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no worries, I realised I got both PRs mixed up 🫠


// Compress the normalized VCF files with bgzip
TABIX_EXT_VCF(GERMLINE_VCFS_NORM.out.vcf)

// Index the compressed normalized VCF files
TABIX_GERMLINE_VCFS_CONCAT_SORT(TABIX_EXT_VCF.out.gz)

// Gather vcfs and vcf-tbis for concatenating germline-vcfs
germline_vcfs_with_tbis = TABIX_EXT_VCF.out.gz_tbi.map{ meta, vcf, tbi -> [ meta.subMap('id'), vcf, tbi ] }.groupTuple()
germline_vcfs_with_tbis = TABIX_GERMLINE_VCFS_CONCAT_SORT.out.map { meta, vcf, tbi -> [meta.subMap('id'), vcf, tbi] }.groupTuple()

// Concatenate the VCF files
GERMLINE_VCFS_CONCAT(germline_vcfs_with_tbis)

// Sort the concatenated VCF files
GERMLINE_VCFS_CONCAT_SORT(GERMLINE_VCFS_CONCAT.out.vcf)

// Index the sorted concatenated VCF files
TABIX_GERMLINE_VCFS_CONCAT_SORT(GERMLINE_VCFS_CONCAT_SORT.out.vcf)

// Gather versions of all tools used
versions = versions.mix(ADD_INFO_TO_VCF.out.versions)
versions = versions.mix(TABIX_EXT_VCF.out.versions)
versions = versions.mix(GERMLINE_VCFS_NORM.out.versions)
versions = versions.mix(GERMLINE_VCFS_CONCAT.out.versions)
versions = versions.mix(GERMLINE_VCFS_CONCAT.out.versions)
versions = versions.mix(GERMLINE_VCFS_CONCAT_SORT.out.versions)
versions = versions.mix(TABIX_GERMLINE_VCFS_CONCAT_SORT.out.versions)

emit:
vcfs = germline_vcfs_with_tbis // post processed vcfs

vcfs = TABIX_GERMLINE_VCFS_CONCAT_SORT.out.gz_tbi // post-processed VCFs
versions // channel: [ versions.yml ]
}

3 changes: 2 additions & 1 deletion workflows/sarek/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -794,7 +794,8 @@ workflow SAREK {

// POST VARIANTCALLING
POST_VARIANTCALLING(BAM_VARIANT_CALLING_GERMLINE_ALL.out.vcf_all,
params.concatenate_vcfs)
fasta,
params.concatenate_vcfs)

// Gather vcf files for annotation and QC
vcf_to_annotate = Channel.empty()
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