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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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2 changes: 1 addition & 1 deletion 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 @@ -15,7 +15,7 @@ workflow POST_VARIANTCALLING {
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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47 changes: 29 additions & 18 deletions subworkflows/local/vcf_concatenate_germline/main.nf
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Original file line number Diff line number Diff line change
@@ -1,14 +1,12 @@
//
// 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_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'
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 {

Expand All @@ -19,30 +17,43 @@ workflow CONCATENATE_GERMLINE_VCFS {
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)

// Normalize vcf-files and concat
GERMLINE_VCFS_NORM(germline_vcfs_with_tbis, fasta)
GERMLINE_VCFS_CONCAT(GERMLINE_VCFS_NORM.out.vcf)
// Sort the concatenated VCF files
GERMLINE_VCFS_CONCAT_SORT(GERMLINE_VCFS_CONCAT.out.vcf)
TABIX_GERMLINE_VCFS_CONCAT_SORT(GERMLINE_VCFS_CONCAT_SORT.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 ]
}