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2 changes: 1 addition & 1 deletion .github/workflows/ci.yml
Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ jobs:
matrix:
NXF_VER:
- "24.10.0"
- "latest-everything"
- "latest-stable"
filter:
- "process"
- "workflow"
Expand Down
52 changes: 26 additions & 26 deletions .nf-core.yml
Original file line number Diff line number Diff line change
Expand Up @@ -2,32 +2,32 @@ bump_version:
lint:
actions_ci: false
files_exist:
- CODE_OF_CONDUCT.md
- assets/nf-core-germline_logo_light.png
- docs/images/nf-core-germline_logo_light.png
- docs/images/nf-core-germline_logo_dark.png
- .github/ISSUE_TEMPLATE/config.yml
- .github/workflows/awstest.yml
- .github/workflows/awsfulltest.yml
- .github/workflows/template_version_comment.yml
- docs/README.md
- CODE_OF_CONDUCT.md
- assets/nf-core-germline_logo_light.png
- docs/images/nf-core-germline_logo_light.png
- docs/images/nf-core-germline_logo_dark.png
- .github/ISSUE_TEMPLATE/config.yml
- .github/workflows/awstest.yml
- .github/workflows/awsfulltest.yml
- .github/workflows/template_version_comment.yml
- docs/README.md
files_unchanged:
- .github/CONTRIBUTING.md
- .github/PULL_REQUEST_TEMPLATE.md
- .github/workflows/branch.yml
- .github/workflows/linting_comment.yml
- .github/workflows/linting.yml
- CODE_OF_CONDUCT.md
- .github/ISSUE_TEMPLATE/bug_report.yml
- .prettierignore
- .github/CONTRIBUTING.md
- .github/PULL_REQUEST_TEMPLATE.md
- .github/workflows/branch.yml
- .github/workflows/linting_comment.yml
- .github/workflows/linting.yml
- CODE_OF_CONDUCT.md
- .github/ISSUE_TEMPLATE/bug_report.yml
- .prettierignore
multiqc_config:
- report_comment
- report_comment
nextflow_config:
- custom_config
- manifest.name
- manifest.homePage
- validation.help.afterText
- validation.summary.afterText
- custom_config
- manifest.name
- manifest.homePage
- validation.help.afterText
- validation.summary.afterText
subworkflow_changes: false
nf_core_version: 3.0.2
repository_type: pipeline
Expand All @@ -41,6 +41,6 @@ template:
org: nf-cmgg
outdir: .
skip_features:
- fastqc
- is_nfcore
version: 1.9.1
- fastqc
- is_nfcore
version: 1.9.2
7 changes: 7 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,13 @@
The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).

## v1.9.2 - New Nieuwkerke - [January 22 2025]

## Changes

1. The pipeline now also outputs the per-base coverage BED file generated by mosdepth per sample
2. Add the `--disable_hc_dict_validation` parameter that disables sequence dictionary validation in HaplotypeCaller

## v1.9.1 - Nice Nieuwkerke - [January 16 2025]

### Changes
Expand Down
5 changes: 3 additions & 2 deletions conf/modules.config
Original file line number Diff line number Diff line change
Expand Up @@ -44,7 +44,7 @@ process {

withName: "^.*CRAM_PREPARE_SAMTOOLS_BEDTOOLS:MOSDEPTH\$" {
ext.args = [
"--quantize 0:1:${params.min_callable_coverage - 1}: --mapq 1 --flag 1804 --no-per-base",
"--quantize 0:1:${params.min_callable_coverage - 1}: --mapq 1 --flag 1804",
params.mosdepth_slow ? "" : "--fast-mode"
].join(" ")
}
Expand Down Expand Up @@ -79,7 +79,8 @@ process {
'-GQB 10 -GQB 20 -GQB 30 -GQB 40 -GQB 50 -GQB 60 -GQB 70 -GQB 80 -GQB 90',
'-G StandardAnnotation -G StandardHCAnnotation -G AS_StandardAnnotation',
params.dragstr ? '--dragen-mode' : '',
params.hc_phasing ? '' : '--do-not-run-physical-phasing'
params.hc_phasing ? '' : '--do-not-run-physical-phasing',
params.disable_hc_dict_validation ? '--disable-sequence-dictionary-validation' : ''
].join(" ")
}
}
Expand Down
25 changes: 13 additions & 12 deletions conf/seqplorer.config
Original file line number Diff line number Diff line change
Expand Up @@ -5,18 +5,19 @@
*/

params {
filter = true
normalize = true
gemini = true
filter = true
normalize = true
gemini = true
disable_hc_dict_validation = true

vcfanno = true
annotate = true
vep_merged = true
vep_spliceai = true
vep_mastermind = true
vep_eog = true
vep_spliceregion = true
vcfanno = true
annotate = true
vep_merged = true
vep_spliceai = true
vep_mastermind = true
vep_eog = true
vep_spliceregion = true

vcfanno_config = "https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-configs/main/conf/Hsapiens/vcfanno/cmgg_vcfanno.toml"
vcfanno_resources = "${params.genomes_base}/Hsapiens/GRCh38/variation/dbscSNV-1.1/dbscSNV.txt.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/dbscSNV-1.1/dbscSNV.txt.gz.tbi;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/exomes/r2.2.1/gnomad_exomes.vcf.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/exomes/r2.2.1/gnomad_exomes.vcf.gz.csi;${params.genomes_base}/Hsapiens/GRCh38/variation/clinvar/clinvar_20221119.vcf.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/clinvar/clinvar_20221119.vcf.gz.tbi;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/genomes/r3.1.2/gnomad_genomes.vcf.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/genomes/r3.1.2/gnomad_genomes.vcf.gz.csi;${params.genomes_base}/Hsapiens/GRCh38/variation/dbNSFP-4.3/dbNSFP4.3a_grch38.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/dbNSFP-4.3/dbNSFP4.3a_grch38.gz.tbi"
vcfanno_config = "https://raw.githubusercontent.com/CenterForMedicalGeneticsGhent/nf-cmgg-configs/main/conf/Hsapiens/vcfanno/cmgg_vcfanno.toml"
vcfanno_resources = "${params.genomes_base}/Hsapiens/GRCh38/variation/dbscSNV-1.1/dbscSNV.txt.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/dbscSNV-1.1/dbscSNV.txt.gz.tbi;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/exomes/r2.2.1/gnomad_exomes.vcf.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/exomes/r2.2.1/gnomad_exomes.vcf.gz.csi;${params.genomes_base}/Hsapiens/GRCh38/variation/clinvar/clinvar_20221119.vcf.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/clinvar/clinvar_20221119.vcf.gz.tbi;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/genomes/r3.1.2/gnomad_genomes.vcf.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/gnomAD/genomes/r3.1.2/gnomad_genomes.vcf.gz.csi;${params.genomes_base}/Hsapiens/GRCh38/variation/dbNSFP-4.3/dbNSFP4.3a_grch38.gz;${params.genomes_base}/Hsapiens/GRCh38/variation/dbNSFP-4.3/dbNSFP4.3a_grch38.gz.tbi"
}
6 changes: 6 additions & 0 deletions docs/output.md
Original file line number Diff line number Diff line change
Expand Up @@ -34,6 +34,8 @@ To explain the structure of the output directory, a simple example run consistin
│ │ ├── sample1.<caller>.bcftools_stats.txt #(17)!
│ │ ├── sample1.<caller>.g.vcf.gz #(18)!
│ │ ├── sample1.<caller>.g.vcf.gz.tbi #(19)!
│ │ ├── sample1.per-base.bed.gz #(33)!
│ │ ├── sample1.per-base.bed.gz.csi #(34)!
│ │ └── validation #(20)!
│ │ └── <caller> #(21)!
│ │ ├── ... #(22)!
Expand Down Expand Up @@ -118,3 +120,7 @@ To explain the structure of the output directory, a simple example run consistin
31. This file contains a list of all tools used in the pipeline and their versions

32. The samplesheet used to run this pipeline run

33. The per-base coverage BED file generated by Mosdepth

34. The index of the per-base coverage BED file generated by Mosdepth
13 changes: 9 additions & 4 deletions main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -99,10 +99,6 @@ workflow {
if(!(caller in GlobalVariables.availableCallers)) { error("\"${caller}\" is not a supported callers please use one or more of these instead: ${GlobalVariables.availableCallers}")}
}

if (params.output_suffix && callers.size() > 1) {
error("Cannot use --output_suffix with more than one caller")
}

/*
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
CONFIG FILES
Expand Down Expand Up @@ -219,6 +215,7 @@ workflow {
publish:
ch_gvcfs_out >> 'gvcfs'
GERMLINE.out.single_beds >> 'single_beds'
GERMLINE.out.perbase_beds >> 'perbase_beds'
GERMLINE.out.validation >> 'validation'
GERMLINE.out.gvcf_reports >> 'gvcf_reports'
GERMLINE.out.genomicsdb >> 'genomicsdb'
Expand All @@ -245,6 +242,14 @@ output {
'single_beds' {
path { meta, _bed -> { _file -> "${meta.family}/${meta.id}_${params.unique_out}/${meta.id}.bed" } }
}
'perbase_beds' {
path { meta, bed, _csi -> { file ->
if(file == bed.name) {
return "${meta.family}/${meta.id}_${params.unique_out}/${meta.id}.per-base.bed.gz"
}
return "${meta.family}/${meta.id}_${params.unique_out}/${meta.id}.per-base.bed.gz.csi"
} }
}
'validation' {
path { meta, _report -> { file -> "${meta.family}/${meta.id}_${params.unique_out}/validation/${meta.caller}/${file}" } }
}
Expand Down
3 changes: 2 additions & 1 deletion nextflow.config
Original file line number Diff line number Diff line change
Expand Up @@ -41,6 +41,7 @@ params {
mosdepth_slow = false
merge_distance = 100000
updio_common_cnvs = null
disable_hc_dict_validation = false

// VEP plugins to use
vep_dbnsfp = false
Expand Down Expand Up @@ -276,7 +277,7 @@ manifest {
description = """A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data"""
mainScript = 'main.nf'
nextflowVersion = '!>=24.10.0'
version = '1.9.1'
version = '1.9.2'
doi = ''
}

Expand Down
4 changes: 4 additions & 0 deletions nextflow_schema.json
Original file line number Diff line number Diff line change
Expand Up @@ -331,6 +331,10 @@
"type": "string",
"description": "Don't change this value",
"hidden": true
},
"disable_hc_dict_validation": {
"type": "boolean",
"description": "Disable the sequence dictionary validation in HaplotypeCaller"
}
}
},
Expand Down
13 changes: 8 additions & 5 deletions subworkflows/local/cram_prepare_samtools_bedtools/main.nf
Original file line number Diff line number Diff line change
Expand Up @@ -151,6 +151,8 @@ workflow CRAM_PREPARE_SAMTOOLS_BEDTOOLS {
ch_fasta
)
ch_versions = ch_versions.mix(MOSDEPTH.out.versions.first())
def ch_perbase_beds = MOSDEPTH.out.per_base_bed
.join(MOSDEPTH.out.per_base_csi, failOnMismatch: true, failOnDuplicate:true)

def ch_beds_to_filter = ch_ready_rois
.join(MOSDEPTH.out.quantized_bed, failOnDuplicate:true, failOnMismatch:true)
Expand Down Expand Up @@ -181,9 +183,10 @@ workflow CRAM_PREPARE_SAMTOOLS_BEDTOOLS {
.mix(BEDTOOLS_INTERSECT.out.intersect)

emit:
ready_crams = ch_ready_crams // [ val(meta), path(cram), path(crai) ]
ready_bams = ch_ready_bams // [ val(meta), path(bam), path(bai) ]
ready_beds = ch_ready_beds // [ val(meta), path(bed) ]
versions = ch_versions // [ path(versions) ]
reports = ch_reports // [ path(reports) ]
ready_crams = ch_ready_crams // [ val(meta), path(cram), path(crai) ]
ready_bams = ch_ready_bams // [ val(meta), path(bam), path(bai) ]
ready_beds = ch_ready_beds // [ val(meta), path(bed) ]
perbase_beds = ch_perbase_beds // [ val(meta), path(bed), path(csi) ]
versions = ch_versions // [ path(versions) ]
reports = ch_reports // [ path(reports) ]
}
Original file line number Diff line number Diff line change
Expand Up @@ -48,6 +48,7 @@ nextflow_workflow {
[ it[0], "${file(it[1]).name},readsMD5:${bam(it[1]).getReadsMD5()}", file(it[2]).name ]
},
workflow.out.ready_beds,
workflow.out.perbase_beds,
workflow.out.reports
).match() }
)
Expand Down Expand Up @@ -95,6 +96,7 @@ nextflow_workflow {
[ it[0], "${file(it[1]).name},readsMD5:${bam(it[1]).getReadsMD5()}", file(it[2]).name ]
},
workflow.out.ready_beds,
workflow.out.perbase_beds,
workflow.out.reports
).match() }
)
Expand Down Expand Up @@ -142,6 +144,7 @@ nextflow_workflow {
[ it[0], "${file(it[1]).name},readsMD5:${bam(it[1]).getReadsMD5()}", file(it[2]).name ]
},
workflow.out.ready_beds,
workflow.out.perbase_beds,
workflow.out.reports
).match() }
)
Expand Down Expand Up @@ -196,6 +199,7 @@ nextflow_workflow {
[ it[0], "${file(it[1]).name},readsMD5:${bam(it[1]).getReadsMD5()}", file(it[2]).name ]
},
workflow.out.ready_beds,
workflow.out.perbase_beds,
workflow.out.reports
).match() }
)
Expand Down
Original file line number Diff line number Diff line change
Expand Up @@ -39,15 +39,28 @@
"NA24143.intersect.bed:md5,b87069698afefb15282d069e56110046"
]
],
[
[
{
"id": "NA24143",
"sample": "NA24143",
"family": "Ashkenazim",
"family_samples": "NA24143",
"duplicate_count": 1
},
"NA24143.per-base.bed.gz:md5,2f773324021d6d1b18c87af240d1a18f",
"NA24143.per-base.bed.gz.csi:md5,fe996e285822f6126adcdca8b7517058"
]
],
[

]
],
"meta": {
"nf-test": "0.9.1",
"nextflow": "24.10.0"
"nextflow": "24.10.3"
},
"timestamp": "2024-11-14T16:07:03.620603158"
"timestamp": "2025-01-22T13:39:12.575142149"
},
"cram_prepare_samtools_bedtools - default - WES": {
"content": [
Expand Down Expand Up @@ -79,15 +92,28 @@
"NA24143.intersect.bed:md5,b87069698afefb15282d069e56110046"
]
],
[
[
{
"id": "NA24143",
"sample": "NA24143",
"family": "Ashkenazim",
"family_samples": "NA24143",
"duplicate_count": 1
},
"NA24143.per-base.bed.gz:md5,2f773324021d6d1b18c87af240d1a18f",
"NA24143.per-base.bed.gz.csi:md5,fe996e285822f6126adcdca8b7517058"
]
],
[

]
],
"meta": {
"nf-test": "0.9.1",
"nextflow": "24.10.0"
"nextflow": "24.10.3"
},
"timestamp": "2024-11-14T16:07:24.688580575"
"timestamp": "2025-01-22T13:39:30.958080052"
},
"cram_prepare_samtools_bedtools - default - WGS": {
"content": [
Expand Down Expand Up @@ -119,15 +145,28 @@
"NA24143.filter.bed:md5,85a5568a6976ed455caa712991b30ac2"
]
],
[
[
{
"id": "NA24143",
"sample": "NA24143",
"family": "Ashkenazim",
"family_samples": "NA24143",
"duplicate_count": 1
},
"NA24143.per-base.bed.gz:md5,2f773324021d6d1b18c87af240d1a18f",
"NA24143.per-base.bed.gz.csi:md5,fe996e285822f6126adcdca8b7517058"
]
],
[

]
],
"meta": {
"nf-test": "0.9.1",
"nextflow": "24.10.0"
"nextflow": "24.10.3"
},
"timestamp": "2024-11-14T16:06:42.311563291"
"timestamp": "2025-01-22T13:38:51.625657423"
},
"cram_prepare_samtools_bedtools - default - merge": {
"content": [
Expand Down Expand Up @@ -169,14 +208,27 @@
"NA24143.intersect.bed:md5,b87069698afefb15282d069e56110046"
]
],
[
[
{
"id": "NA24143",
"sample": "NA24143",
"family": "Ashkenazim",
"family_samples": "NA24143",
"duplicate_count": 2
},
"NA24143.per-base.bed.gz:md5,85e799ea056ba8d127115e012adcbe7a",
"NA24143.per-base.bed.gz.csi:md5,3f40731dbdbef353385d04f51feb43b3"
]
],
[

]
],
"meta": {
"nf-test": "0.9.1",
"nextflow": "24.10.0"
"nextflow": "24.10.3"
},
"timestamp": "2024-11-14T16:08:20.712943795"
"timestamp": "2025-01-22T13:40:12.40700375"
}
}
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