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FriederikeHanssenFriederikeHanssen
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indent things, clean up, add comments, consolidate
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-219
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‎conf/modules/aligner.config

+7-30
Original file line numberDiff line numberDiff line change
@@ -33,13 +33,7 @@ process {
3333
ext.when = { params.aligner == "sentieon-bwamem" }
3434
}
3535

36-
37-
38-
withName: "(BWAMEM.*_MEM|DRAGMAP_ALIGN)" {
39-
// Markduplicates Spark NEEDS name-sorted reads or runtime goes through the roof
40-
// However if it's skipped, reads need to be coordinate-sorted
41-
// Only name sort if Spark for Markduplicates + duplicate marking is not skipped
42-
ext.args2 = { params.use_gatk_spark && params.use_gatk_spark.contains('markduplicates') && (!params.skip_tools || (params.skip_tools && !params.skip_tools.split(',').contains('markduplicates'))) ? '-n' : '' }
36+
withName: "(BWAMEM.*_MEM|DRAGMAP_ALIGN|SENTIEON_BWAMEM)" {
4337
ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.tokenize('.')[0]) : "${meta.id}.sorted" }
4438
publishDir = [
4539
mode: params.publish_dir_mode,
@@ -61,29 +55,12 @@ process {
6155
]
6256
}
6357

64-
65-
withName: "SENTIEON_BWAMEM" {
66-
// Markduplicates Spark NEEDS name-sorted reads or runtime goes through the roof.
67-
// However, currently SENTIEON_BWAMEM only supports coordinate sorting the reads.
68-
ext.prefix = { params.split_fastq > 1 ? "${meta.id}".concat('.').concat(reads.get(0).name.tokenize('.')[0]) : "${meta.id}.sorted" }
69-
publishDir = [
70-
mode: params.publish_dir_mode,
71-
path: { "${params.outdir}/preprocessing/" },
72-
pattern: "*bam",
73-
// Only save if save_output_as_bam AND
74-
// (save_mapped OR no_markduplicates OR sentieon_dedup) AND
75-
// only a single BAM file per sample
76-
saveAs: {
77-
if (params.save_output_as_bam &&
78-
(
79-
params.save_mapped ||
80-
(params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) &&
81-
!(params.tools && params.tools.split(',').contains('sentieon_dedup'))
82-
) && (meta.size * meta.num_lanes == 1)
83-
) { "mapped/${meta.id}/${it}" }
84-
else { null }
85-
}
86-
]
58+
withName: "(BWAMEM.*_MEM|DRAGMAP_ALIGN)" {
59+
// Markduplicates Spark NEEDS name-sorted reads or runtime goes through the roof
60+
// However if it's skipped, reads need to be coordinate-sorted
61+
// Only name sort if Spark for Markduplicates + duplicate marking is not skipped
62+
// Currently SENTIEON_BWAMEM only supports coordinate sorting the reads.
63+
ext.args2 = { params.use_gatk_spark && params.use_gatk_spark.contains('markduplicates') && (!params.skip_tools || (params.skip_tools && !params.skip_tools.split(',').contains('markduplicates'))) ? '-n' : '' }
8764
}
8865

8966
withName: "BWAMEM.*_MEM|SENTIEON_BWAMEM" {

‎conf/modules/mutect2.config

+1
Original file line numberDiff line numberDiff line change
@@ -15,6 +15,7 @@
1515

1616
process {
1717
if (params.tools && params.tools.split(',').contains('mutect2')) {
18+
1819
withName: 'GATK4_MUTECT2' {
1920
ext.prefix = { meta.num_intervals <= 1 ? "${meta.id}.mutect2" : "${meta.id}.mutect2.${intervals.simpleName}" }
2021
ext.when = { params.tools && params.tools.split(',').contains('mutect2') }

‎conf/modules/post_variant_calling.config

+1
Original file line numberDiff line numberDiff line change
@@ -15,6 +15,7 @@
1515
// Like, for instance, concatenating the unannotated, germline vcf-files
1616

1717
process {
18+
1819
withName: 'GERMLINE_VCFS_CONCAT'{
1920
publishDir = [
2021
//specify to avoid publishing, overwritten otherwise

‎conf/modules/prepare_cache.config

+1
Original file line numberDiff line numberDiff line change
@@ -14,6 +14,7 @@
1414
// PREPARE_CACHE
1515

1616
process {
17+
1718
// SNPEFF
1819
withName: 'SNPEFF_DOWNLOAD' {
1920
ext.when = { params.tools && (params.tools.split(',').contains('snpeff') || params.tools.split(',').contains('merge')) }

‎conf/modules/umi.config

+1
Original file line numberDiff line numberDiff line change
@@ -62,6 +62,7 @@ process {
6262
enabled: false
6363
]
6464
}
65+
6566
withName: 'GROUPREADSBYUMI' {
6667
publishDir = [
6768
[ path: { "${params.outdir}/reports/umi/" },

‎docs/usage.md

+5-5
Original file line numberDiff line numberDiff line change
@@ -1023,11 +1023,6 @@ Enable with `--vep_spliceregion`.
10231023
10241024
For more details, see [here](https://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#spliceregion) and [here](https://www.ensembl.info/2018/10/26/cool-stuff-the-vep-can-do-splice-site-variant-annotation/)."
10251025
1026-
## Requested resources for the tools
1027-
1028-
Resource requests are difficult to generalize and are often dependent on input data size. Currently, the number of cpus and memory requested by default were adapted from tests on 5 ICGC paired whole-genome sequencing samples with approximately 40X and 80X depth.
1029-
For targeted data analysis, this is overshooting by a lot. In this case resources for each process can be limited by either setting `--max_memory` and `-max_cpus` or tailoring the request by process name as described [here](#resource-requests). If you are using sarek for a certain data type regulary, and would like to make these requests available to others on your system, an institution-specific, pipeline-specific config file can be added [here](https://github.com/nf-core/configs/tree/master/conf/pipeline/sarek).
1030-
10311026
## MultiQC related issues
10321027
10331028
### Plots for SnpEff are missing
@@ -1050,3 +1045,8 @@ Sentieon's [GVCFtyper](https://support.sentieon.com/manual/usages/general/#gvcft
10501045
### QualCal (BQSR)
10511046
10521047
Currently, Sentieon's version of BQSR, QualCal, is not available in Sarek. Recent Illumina sequencers tend to provide well-calibrated BQs, so BQSR may not provide much benefit. By default Sarek runs GATK's BQSR; that can be skipped by adding the option `--skip_tools baserecalibrator`.
1048+
1049+
## Requested resources for the tools
1050+
1051+
Resource requests are difficult to generalize and are often dependent on input data size. Currently, the number of cpus and memory requested by default were adapted from tests on 5 ICGC paired whole-genome sequencing samples with approximately 40X and 80X depth.
1052+
For targeted data analysis, this is overshooting by a lot. In this case resources for each process can be limited by either setting `--max_memory` and `-max_cpus` or tailoring the request by process name as described [here](#resource-requests). If you are using sarek for a certain data type regulary, and would like to make these requests available to others on your system, an institution-specific, pipeline-specific config file can be added [here](https://github.com/nf-core/configs/tree/master/conf/pipeline/sarek).

‎subworkflows/local/bam_convert_samtools/main.nf

+8-8
Original file line numberDiff line numberDiff line change
@@ -2,14 +2,14 @@
22
// BAM/CRAM to FASTQ conversion, paired end only
33
//
44

5-
include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_MAP_MAP } from '../../../modules/nf-core/samtools/view/main'
6-
include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_UNMAP_UNMAP } from '../../../modules/nf-core/samtools/view/main'
7-
include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_UNMAP_MAP } from '../../../modules/nf-core/samtools/view/main'
8-
include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_MAP_UNMAP } from '../../../modules/nf-core/samtools/view/main'
9-
include { SAMTOOLS_MERGE as SAMTOOLS_MERGE_UNMAP } from '../../../modules/nf-core/samtools/merge/main'
10-
include { SAMTOOLS_COLLATEFASTQ as COLLATE_FASTQ_UNMAP } from '../../../modules/nf-core/samtools/collatefastq/main'
11-
include { SAMTOOLS_COLLATEFASTQ as COLLATE_FASTQ_MAP } from '../../../modules/nf-core/samtools/collatefastq/main'
12-
include { CAT_FASTQ } from '../../../modules/nf-core/cat/fastq/main'
5+
include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_MAP_MAP } from '../../../modules/nf-core/samtools/view/main'
6+
include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_UNMAP_UNMAP } from '../../../modules/nf-core/samtools/view/main'
7+
include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_UNMAP_MAP } from '../../../modules/nf-core/samtools/view/main'
8+
include { SAMTOOLS_VIEW as SAMTOOLS_VIEW_MAP_UNMAP } from '../../../modules/nf-core/samtools/view/main'
9+
include { SAMTOOLS_MERGE as SAMTOOLS_MERGE_UNMAP } from '../../../modules/nf-core/samtools/merge/main'
10+
include { SAMTOOLS_COLLATEFASTQ as COLLATE_FASTQ_UNMAP } from '../../../modules/nf-core/samtools/collatefastq/main'
11+
include { SAMTOOLS_COLLATEFASTQ as COLLATE_FASTQ_MAP } from '../../../modules/nf-core/samtools/collatefastq/main'
12+
include { CAT_FASTQ } from '../../../modules/nf-core/cat/fastq/main'
1313

1414
workflow BAM_CONVERT_SAMTOOLS {
1515
take:

‎subworkflows/local/bam_joint_calling_germline_gatk/main.nf

+9-5
Original file line numberDiff line numberDiff line change
@@ -1,12 +1,16 @@
11
//
2-
// merge samples with genomicsdbimport, perform joint genotyping with genotypeGVCFS
2+
// JOINT GERMLINE CALLING
3+
//
4+
// Merge samples with genomicsdbimport, perform joint genotyping with genotypeGVCFS
5+
//
6+
37
include { BCFTOOLS_SORT } from '../../../modules/nf-core/bcftools/sort/main'
4-
include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_INDEL } from '../../../modules/nf-core/gatk4/applyvqsr/main'
5-
include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_SNP } from '../../../modules/nf-core/gatk4/applyvqsr/main'
8+
include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_INDEL } from '../../../modules/nf-core/gatk4/applyvqsr/main'
9+
include { GATK4_APPLYVQSR as GATK4_APPLYVQSR_SNP } from '../../../modules/nf-core/gatk4/applyvqsr/main'
610
include { GATK4_GENOMICSDBIMPORT } from '../../../modules/nf-core/gatk4/genomicsdbimport/main'
711
include { GATK4_GENOTYPEGVCFS } from '../../../modules/nf-core/gatk4/genotypegvcfs/main'
8-
include { GATK4_MERGEVCFS as MERGE_GENOTYPEGVCFS } from '../../../modules/nf-core/gatk4/mergevcfs/main'
9-
include { GATK4_MERGEVCFS as MERGE_VQSR } from '../../../modules/nf-core/gatk4/mergevcfs/main'
12+
include { GATK4_MERGEVCFS as MERGE_GENOTYPEGVCFS } from '../../../modules/nf-core/gatk4/mergevcfs/main'
13+
include { GATK4_MERGEVCFS as MERGE_VQSR } from '../../../modules/nf-core/gatk4/mergevcfs/main'
1014
include { GATK4_VARIANTRECALIBRATOR as VARIANTRECALIBRATOR_INDEL } from '../../../modules/nf-core/gatk4/variantrecalibrator/main'
1115
include { GATK4_VARIANTRECALIBRATOR as VARIANTRECALIBRATOR_SNP } from '../../../modules/nf-core/gatk4/variantrecalibrator/main'
1216

‎subworkflows/local/bam_joint_calling_germline_sentieon/main.nf

+14-8
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,17 @@
1-
include { BCFTOOLS_SORT } from '../../../modules/nf-core/bcftools/sort/main'
2-
include { SENTIEON_APPLYVARCAL as SENTIEON_APPLYVARCAL_INDEL } from '../../../modules/nf-core/sentieon/applyvarcal/main'
3-
include { SENTIEON_APPLYVARCAL as SENTIEON_APPLYVARCAL_SNP } from '../../../modules/nf-core/sentieon/applyvarcal/main'
4-
include { SENTIEON_GVCFTYPER } from '../../../modules/nf-core/sentieon/gvcftyper/main'
5-
include { GATK4_MERGEVCFS as MERGE_GENOTYPEGVCFS } from '../../../modules/nf-core/gatk4/mergevcfs/main'
6-
include { GATK4_MERGEVCFS as MERGE_VQSR } from '../../../modules/nf-core/gatk4/mergevcfs/main'
7-
include { SENTIEON_VARCAL as SENTIEON_VARCAL_INDEL } from '../../../modules/nf-core/sentieon/varcal/main'
8-
include { SENTIEON_VARCAL as SENTIEON_VARCAL_SNP } from '../../../modules/nf-core/sentieon/varcal/main'
1+
//
2+
// JOINT GERMLINE CALLING
3+
//
4+
// Merge samples perform joint genotyping with SENTIEON_GVCFTYPER
5+
//
6+
7+
include { BCFTOOLS_SORT } from '../../../modules/nf-core/bcftools/sort/main'
8+
include { GATK4_MERGEVCFS as MERGE_GENOTYPEGVCFS } from '../../../modules/nf-core/gatk4/mergevcfs/main'
9+
include { GATK4_MERGEVCFS as MERGE_VQSR } from '../../../modules/nf-core/gatk4/mergevcfs/main'
10+
include { SENTIEON_APPLYVARCAL as SENTIEON_APPLYVARCAL_INDEL } from '../../../modules/nf-core/sentieon/applyvarcal/main'
11+
include { SENTIEON_APPLYVARCAL as SENTIEON_APPLYVARCAL_SNP } from '../../../modules/nf-core/sentieon/applyvarcal/main'
12+
include { SENTIEON_GVCFTYPER } from '../../../modules/nf-core/sentieon/gvcftyper/main'
13+
include { SENTIEON_VARCAL as SENTIEON_VARCAL_INDEL } from '../../../modules/nf-core/sentieon/varcal/main'
14+
include { SENTIEON_VARCAL as SENTIEON_VARCAL_SNP } from '../../../modules/nf-core/sentieon/varcal/main'
915

1016
workflow BAM_JOINT_CALLING_GERMLINE_SENTIEON {
1117
take:

‎subworkflows/local/bam_markduplicates/main.nf

+3-3
Original file line numberDiff line numberDiff line change
@@ -1,11 +1,11 @@
11
//
2-
// MARKDUPLICATES
2+
// MARKDUPLICATES AND QC after mapping
33
//
44
// For all modules here:
55
// A when clause condition is defined in the conf/modules.config to determine if the module should be run
66

7-
include { CRAM_QC_MOSDEPTH_SAMTOOLS } from '../cram_qc_mosdepth_samtools/main'
8-
include { GATK4_MARKDUPLICATES } from '../../../modules/nf-core/gatk4/markduplicates/main'
7+
include { CRAM_QC_MOSDEPTH_SAMTOOLS } from '../cram_qc_mosdepth_samtools/main'
8+
include { GATK4_MARKDUPLICATES } from '../../../modules/nf-core/gatk4/markduplicates/main'
99

1010
workflow BAM_MARKDUPLICATES {
1111
take:

‎subworkflows/local/bam_markduplicates_spark/main.nf

+5-5
Original file line numberDiff line numberDiff line change
@@ -1,13 +1,13 @@
11
//
2-
// MARKDUPLICATES AND/OR QC after mapping
2+
// MARKDUPLICATES SPARK AND QC after mapping
33
//
44
// For all modules here:
55
// A when clause condition is defined in the conf/modules.config to determine if the module should be run
66

7-
include { CRAM_QC_MOSDEPTH_SAMTOOLS } from '../cram_qc_mosdepth_samtools/main'
8-
include { GATK4_ESTIMATELIBRARYCOMPLEXITY } from '../../../modules/nf-core/gatk4/estimatelibrarycomplexity/main'
9-
include { GATK4_MARKDUPLICATES_SPARK } from '../../../modules/nf-core/gatk4/markduplicatesspark/main'
10-
include { SAMTOOLS_INDEX as INDEX_MARKDUPLICATES } from '../../../modules/nf-core/samtools/index/main'
7+
include { CRAM_QC_MOSDEPTH_SAMTOOLS } from '../cram_qc_mosdepth_samtools/main'
8+
include { GATK4_ESTIMATELIBRARYCOMPLEXITY } from '../../../modules/nf-core/gatk4/estimatelibrarycomplexity/main'
9+
include { GATK4_MARKDUPLICATES_SPARK } from '../../../modules/nf-core/gatk4/markduplicatesspark/main'
10+
include { SAMTOOLS_INDEX as INDEX_MARKDUPLICATES } from '../../../modules/nf-core/samtools/index/main'
1111

1212
workflow BAM_MARKDUPLICATES_SPARK {
1313
take:

‎subworkflows/local/bam_sentieon_dedup/main.nf

+2-2
Original file line numberDiff line numberDiff line change
@@ -4,8 +4,8 @@
44
// For all modules here:
55
// A when clause condition is defined in the conf/modules.config to determine if the module should be run
66

7-
include { CRAM_QC_MOSDEPTH_SAMTOOLS } from '../cram_qc_mosdepth_samtools/main'
8-
include { SENTIEON_DEDUP } from '../../../modules/nf-core/sentieon/dedup/main'
7+
include { CRAM_QC_MOSDEPTH_SAMTOOLS } from '../cram_qc_mosdepth_samtools/main'
8+
include { SENTIEON_DEDUP } from '../../../modules/nf-core/sentieon/dedup/main'
99

1010
workflow BAM_SENTIEON_DEDUP {
1111
take:

‎subworkflows/local/bam_variant_calling_cnvkit/main.nf

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
//
2-
// CNVKit calling
2+
// CNVKIT calling
33
//
44
// For all modules here:
55
// A when clause condition is defined in the conf/modules.config to determine if the module should be run

‎subworkflows/local/bam_variant_calling_deepvariant/main.nf

+7-1
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,12 @@
1+
//
2+
// DEEPVARIANT germline calling
3+
//
4+
// For all modules here:
5+
// A when clause condition is defined in the conf/modules.config to determine if the module should be run
6+
7+
include { DEEPVARIANT } from '../../../modules/nf-core/deepvariant/main'
18
include { GATK4_MERGEVCFS as MERGE_DEEPVARIANT_GVCF } from '../../../modules/nf-core/gatk4/mergevcfs/main'
29
include { GATK4_MERGEVCFS as MERGE_DEEPVARIANT_VCF } from '../../../modules/nf-core/gatk4/mergevcfs/main'
3-
include { DEEPVARIANT } from '../../../modules/nf-core/deepvariant/main'
410

511
// Deepvariant: https://github.com/google/deepvariant/issues/510
612
workflow BAM_VARIANT_CALLING_DEEPVARIANT {

‎subworkflows/local/bam_variant_calling_freebayes/main.nf

+10-4
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,13 @@
1-
include { BCFTOOLS_SORT } from '../../../modules/nf-core/bcftools/sort/main'
2-
include { GATK4_MERGEVCFS as MERGE_FREEBAYES } from '../../../modules/nf-core/gatk4/mergevcfs/main'
3-
include { FREEBAYES } from '../../../modules/nf-core/freebayes/main'
4-
include { TABIX_TABIX as TABIX_VC_FREEBAYES } from '../../../modules/nf-core/tabix/tabix/main'
1+
//
2+
// FREEBAYES variant calling
3+
//
4+
// For all modules here:
5+
// A when clause condition is defined in the conf/modules.config to determine if the module should be run
6+
7+
include { BCFTOOLS_SORT } from '../../../modules/nf-core/bcftools/sort/main'
8+
include { FREEBAYES } from '../../../modules/nf-core/freebayes/main'
9+
include { GATK4_MERGEVCFS as MERGE_FREEBAYES } from '../../../modules/nf-core/gatk4/mergevcfs/main'
10+
include { TABIX_TABIX as TABIX_VC_FREEBAYES } from '../../../modules/nf-core/tabix/tabix/main'
511

612
workflow BAM_VARIANT_CALLING_FREEBAYES {
713
take:

‎subworkflows/local/bam_variant_calling_germline_all/main.nf

+14-14
Original file line numberDiff line numberDiff line change
@@ -54,7 +54,7 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
5454
vcf_strelka = Channel.empty()
5555
vcf_tiddit = Channel.empty()
5656

57-
// MPILEUP
57+
// BCFTOOLS MPILEUP
5858
if (tools.split(',').contains('mpileup')) {
5959
BAM_VARIANT_CALLING_MPILEUP(
6060
cram,
@@ -153,6 +153,19 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
153153
}
154154
}
155155

156+
// MANTA
157+
if (tools.split(',').contains('manta')) {
158+
BAM_VARIANT_CALLING_GERMLINE_MANTA (
159+
cram,
160+
fasta,
161+
fasta_fai,
162+
intervals_bed_gz_tbi_combined
163+
)
164+
165+
vcf_manta = BAM_VARIANT_CALLING_GERMLINE_MANTA.out.vcf
166+
versions = versions.mix(BAM_VARIANT_CALLING_GERMLINE_MANTA.out.versions)
167+
}
168+
156169
// SENTIEON HAPLOTYPER
157170
if (tools.split(',').contains('sentieon_haplotyper')) {
158171
BAM_VARIANT_CALLING_SENTIEON_HAPLOTYPER(
@@ -202,19 +215,6 @@ workflow BAM_VARIANT_CALLING_GERMLINE_ALL {
202215

203216
}
204217

205-
// MANTA
206-
if (tools.split(',').contains('manta')) {
207-
BAM_VARIANT_CALLING_GERMLINE_MANTA (
208-
cram,
209-
fasta,
210-
fasta_fai,
211-
intervals_bed_gz_tbi_combined
212-
)
213-
214-
vcf_manta = BAM_VARIANT_CALLING_GERMLINE_MANTA.out.vcf
215-
versions = versions.mix(BAM_VARIANT_CALLING_GERMLINE_MANTA.out.versions)
216-
}
217-
218218
// STRELKA
219219
if (tools.split(',').contains('strelka')) {
220220
BAM_VARIANT_CALLING_SINGLE_STRELKA(

‎subworkflows/local/bam_variant_calling_germline_manta/main.nf

+6
Original file line numberDiff line numberDiff line change
@@ -1,3 +1,9 @@
1+
//
2+
// Manta germline variant calling
3+
//
4+
// For all modules here:
5+
// A when clause condition is defined in the conf/modules.config to determine if the module should be run
6+
17
include { MANTA_GERMLINE } from '../../../modules/nf-core/manta/germline/main'
28

39
// Seems to be the consensus on upstream modules implementation too

‎subworkflows/local/bam_variant_calling_haplotypecaller/main.nf

+10-4
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,13 @@
1-
include { BAM_MERGE_INDEX_SAMTOOLS } from '../bam_merge_index_samtools/main'
2-
include { VCF_VARIANT_FILTERING_GATK } from '../vcf_variant_filtering_gatk/main'
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include { GATK4_HAPLOTYPECALLER } from '../../../modules/nf-core/gatk4/haplotypecaller/main'
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include { GATK4_MERGEVCFS as MERGE_HAPLOTYPECALLER } from '../../../modules/nf-core/gatk4/mergevcfs/main'
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//
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// GATK4 HAPLOTYPACALLER germline variant calling:
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//
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// For all modules here:
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// A when clause condition is defined in the conf/modules.config to determine if the module should be run
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include { BAM_MERGE_INDEX_SAMTOOLS } from '../bam_merge_index_samtools/main'
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include { VCF_VARIANT_FILTERING_GATK } from '../vcf_variant_filtering_gatk/main'
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include { GATK4_HAPLOTYPECALLER } from '../../../modules/nf-core/gatk4/haplotypecaller/main'
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include { GATK4_MERGEVCFS as MERGE_HAPLOTYPECALLER } from '../../../modules/nf-core/gatk4/mergevcfs/main'
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workflow BAM_VARIANT_CALLING_HAPLOTYPECALLER {
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take:

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