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add realigned bam export possibilities to gatk4_haplotypecaller #864

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merged 9 commits into from
Nov 24, 2022
Merged

add realigned bam export possibilities to gatk4_haplotypecaller #864

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0a8ad6b
update gatk4/haplotypecaller
maxulysse Nov 24, 2022
59f5fdd
gather realigned bams
maxulysse Nov 24, 2022
83701c2
[automated] Fix linting with Prettier
nf-core-bot Nov 24, 2022
eef1e0f
Merge branch 'dev' into dev_ultima
maxulysse Nov 24, 2022
7d31f4f
fix merge conflicts
maxulysse Nov 24, 2022
80ea7cd
add publish directives for the bam files
maxulysse Nov 24, 2022
0ecea5c
update test tags
maxulysse Nov 24, 2022
5c6017a
fix non-existing channel when joint germline variant calling
maxulysse Nov 24, 2022
16ac8f6
update CHANGELOG
maxulysse Nov 24, 2022
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5 changes: 3 additions & 2 deletions modules.json
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,8 @@
},
"bcftools/mpileup": {
"branch": "master",
"git_sha": "6301e29d77e7ec7ce98b55b8a361b316a9a91bfe"
"git_sha": "6301e29d77e7ec7ce98b55b8a361b316a9a91bfe",
"installed_by": ["modules"]
},
"bcftools/sort": {
"branch": "master",
Expand Down Expand Up @@ -233,7 +234,7 @@
},
"gatk4/haplotypecaller": {
"branch": "master",
"git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67",
"git_sha": "9e9cd1dc1865ee28514c6435e02f1618c091ae20",
"installed_by": ["modules"]
},
"gatk4/intervallisttobed": {
Expand Down
9 changes: 6 additions & 3 deletions modules/nf-core/gatk4/haplotypecaller/main.nf
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4 changes: 4 additions & 0 deletions modules/nf-core/gatk4/haplotypecaller/meta.yml
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30 changes: 28 additions & 2 deletions subworkflows/local/bam_variant_calling_haplotypecaller/main.nf
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Original file line number Diff line number Diff line change
@@ -1,7 +1,8 @@
include { GATK4_MERGEVCFS as MERGE_HAPLOTYPECALLER } from '../../../modules/nf-core/gatk4/mergevcfs/main'
include { GATK4_HAPLOTYPECALLER } from '../../../modules/nf-core/gatk4/haplotypecaller/main'
include { BAM_JOINT_CALLING_GERMLINE_GATK } from '../bam_joint_calling_germline_gatk/main'
include { BAM_MERGE_INDEX_SAMTOOLS } from '../bam_merge_index_samtools/main'
include { VCF_VARIANT_FILTERING_GATK } from '../vcf_variant_filtering_gatk/main'
include { GATK4_HAPLOTYPECALLER } from '../../../modules/nf-core/gatk4/haplotypecaller/main'
include { GATK4_MERGEVCFS as MERGE_HAPLOTYPECALLER } from '../../../modules/nf-core/gatk4/mergevcfs/main'

workflow BAM_VARIANT_CALLING_HAPLOTYPECALLER {
take:
Expand Down Expand Up @@ -42,6 +43,11 @@ workflow BAM_VARIANT_CALLING_HAPLOTYPECALLER {
no_intervals: it[0].num_intervals <= 1
}.set{haplotypecaller_tbi_branch}

GATK4_HAPLOTYPECALLER.out.bam.branch{
intervals: it[0].num_intervals > 1
no_intervals: it[0].num_intervals <= 1
}.set{haplotypecaller_bam_branch}

if (params.joint_germline) {
// merge vcf and tbis
genotype_gvcf_to_call = Channel.empty().mix(GATK4_HAPLOTYPECALLER.out.vcf
Expand Down Expand Up @@ -100,6 +106,25 @@ workflow BAM_VARIANT_CALLING_HAPLOTYPECALLER {
MERGE_HAPLOTYPECALLER.out.tbi,
haplotypecaller_tbi_branch.no_intervals)

// BAM output
BAM_MERGE_INDEX_SAMTOOLS(
haplotypecaller_bam_branch.intervals
.map{ meta, bam ->

new_meta = [
id: meta.sample,
num_intervals: meta.num_intervals,
patient: meta.patient,
sample: meta.sample,
sex: meta.sex,
status: meta.status
]

[groupKey(new_meta, new_meta.num_intervals), bam]
}.groupTuple().mix(haplotypecaller_bam_branch.no_intervals))

realigned_bam = BAM_MERGE_INDEX_SAMTOOLS.out.bam_bai

VCF_VARIANT_FILTERING_GATK(haplotypecaller_vcf.join(haplotypecaller_tbi),
fasta,
fasta_fai,
Expand All @@ -117,4 +142,5 @@ workflow BAM_VARIANT_CALLING_HAPLOTYPECALLER {
emit:
versions = ch_versions
filtered_vcf
realigned_bam
}