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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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1 change: 1 addition & 0 deletions subworkflows/local/post_variantcalling/main.nf
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Well, I've tried an approach, but now I've got a new error:
Process NFCORE_SAREK:SAREK:POST_VARIANTCALLING:CONCATENATE_GERMLINE_VCFS:GERMLINE_VCFS_NORM declares 2 input channels but 1 were specified

-- Check script './workflows/sarek/../../subworkflows/local/post_variantcalling/../vcf_concatenate_germline/main.nf' at line: 27 or see '.nextflow.log' file for more details

I've never done groovy, I think I've broken everything or maybe I'm making it too complex ^^'

Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@ workflow POST_VARIANTCALLING {

take:
vcfs
fasta
concatenate_vcfs

main:
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6 changes: 6 additions & 0 deletions subworkflows/local/vcf_concatenate_germline/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,7 @@
// 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_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'
Expand All @@ -13,10 +14,14 @@ workflow CONCATENATE_GERMLINE_VCFS {

take:
vcfs
fasta

main:
versions = Channel.empty()

// Normalize vcf-files (added by jcdelmas 240415)
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we have a section in the readme collecting all contributors for more visibility. Just add yourself there 🙂 : https://github.com/nf-core/sarek/#credits

GERMLINE_VCFS_NORM(germline_vcfs_with_tbis, fasta)
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I think this might be causing your error. The germline_vcfs+with_tbis is defined further down


// Concatenate vcf-files
ADD_INFO_TO_VCF(vcfs)
TABIX_EXT_VCF(ADD_INFO_TO_VCF.out.vcf)
Expand All @@ -31,6 +36,7 @@ workflow CONCATENATE_GERMLINE_VCFS {
// 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)
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@asp8200 asp8200 Apr 30, 2024 •
edited
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Suggested change
versions = versions.mix(GERMLINE_VCFS_CONCAT.out.versions)
versions = versions.mix(GERMLINE_VCFS_CONCAT_SORT.out.versions)

That seems like a copy-paste bug. Probably my bad

versions = versions.mix(TABIX_GERMLINE_VCFS_CONCAT_SORT.out.versions)
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2 changes: 1 addition & 1 deletion workflows/sarek/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -794,7 +794,7 @@ workflow SAREK {

// POST VARIANTCALLING
POST_VARIANTCALLING(BAM_VARIANT_CALLING_GERMLINE_ALL.out.vcf_all,
params.concatenate_vcfs)
fasta, params.concatenate_vcfs)
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// Gather vcf files for annotation and QC
vcf_to_annotate = Channel.empty()
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