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Merged
famosab merged 4 commits into from
Oct 24, 2025
Merged

Release 3.6.1 #2037

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4228353
Back to dev for 3.7.0dev (#2026)
famosab Oct 14, 2025
65fd802
fix: correct intervals channel for parabricks (#2029)
famosab Oct 23, 2025
6d3e51c
Docs improvement for parabricks (#2038)
famosab Oct 23, 2025
d5f7fe6
fix typo and add note in CHANGELOG (#2039)
famosab Oct 24, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/nf-test.yml
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Expand Up @@ -78,7 +78,7 @@ jobs:
- isMain: false
profile: "singularity"
NXF_VER:
- "24.10.5"
- "25.04.8"
- "latest-everything"
env:
NXF_ANSI_LOG: false
Expand Down
5 changes: 2 additions & 3 deletions .nf-core.yml
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Expand Up @@ -17,11 +17,10 @@ nf_core_version: 3.3.2
repository_type: pipeline
template:
author: Maxime Garcia, Szilveszter Juhos, Friederike Hanssen
description: An open-source analysis pipeline to detect germline or somatic variants
from whole genome or targeted sequencing
description: An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing
force: false
is_nfcore: true
name: sarek
org: nf-core
outdir: .
version: 3.6.0
version: 3.6.1
41 changes: 40 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -5,6 +5,46 @@ All notable changes to this project will be documented in this file.
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).

## [3.6.1](https://github.com/nf-core/sarek/releases/tag/3.6.1) - Sjnjierák

Sjnjierák is a popular stopover cabin on the way into the park.

This patch release includes a bump to Nextflow 25.04.8.

### Added

### Changed

### Fixed

- [2029](https://github.com/nf-core/sarek/pull/2029) - Correct intervals channel for parabricks

### Removed

### Dependencies

| Dependency | Old version | New version |
| ------------ | ----------- | ----------- |
| `parabricks` | 4.5.1-1 | 4.6.0-1 |

### Parameters

| Params | status |
| ------ | ------ |

### Developer section

#### Added

#### Changed

- [2026](https://github.com/nf-core/sarek/pull/2026) - Back to dev
- [2038](https://github.com/nf-core/sarek/pull/2038) - Improve customising parabricks parameters docs

#### Fixed

#### Removed

## [3.6.0](https://github.com/nf-core/sarek/releases/tag/3.6.0) - Kvikkjokk

Kvikkjokk is a village where many trails start that lead through sarek.
Expand Down Expand Up @@ -102,7 +142,6 @@ Kvikkjokk is a village where many trails start that lead through sarek.
| ------------------------------------- | ------ |
| `--freebayes_filter` | New |
| `--msisensor2_models` | New |
| `--msisensor2_scan` | New |
| `--msisensorpro_scan` | New |
| `--sentieon_consensus` | New |
| `--umi_base_skip` | New |
Expand Down
2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -11,7 +11,7 @@
[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.3476425-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.3476425)
[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)

[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
[![Nextflow](https://img.shields.io/badge/version-%E2%89%A525.04.8-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
[![nf-core template version](https://img.shields.io/badge/nf--core_template-3.3.2-green?style=flat&logo=nfcore&logoColor=white&color=%2324B064&link=https%3A%2F%2Fnf-co.re)](https://github.com/nf-core/tools/releases/tag/3.3.2)
[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)
Expand Down
8 changes: 2 additions & 6 deletions assets/multiqc_config.yml
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Expand Up @@ -3,10 +3,7 @@ custom_logo_url: https://github.com/nf-core/sarek/
custom_logo_title: "nf-core/sarek"

report_comment: >
This report has been generated by the <a href="https://github.com/nf-core/sarek/releases/tag/3.6.0"
target="_blank">nf-core/sarek</a> analysis pipeline. For information about how to
interpret these results, please see the <a href="https://nf-co.re/sarek/3.6.0/docs/output"
target="_blank">documentation</a>.
This report has been generated by the <a href="https://github.com/nf-core/sarek/releases/tag/3.6.1" target="_blank">nf-core/sarek</a> analysis pipeline. For information about how to interpret these results, please see the <a href="https://nf-co.re/sarek/3.6.1/docs/output" target="_blank">documentation</a>.
report_section_order:
"nf-core-sarek-methods-description":
order: -1000
Expand Down Expand Up @@ -42,8 +39,7 @@ module_order:
name: "FastP (Read preprocessing)"
- picard:
name: "GATK4 MarkDuplicates"
info: " metrics generated either by GATK4 MarkDuplicates or EstimateLibraryComplexity
(with --use_gatk_spark)."
info: " metrics generated either by GATK4 MarkDuplicates or EstimateLibraryComplexity (with --use_gatk_spark)."
- samtools:
name: "Samtools Flagstat"
- mosdepth:
Expand Down
3 changes: 3 additions & 0 deletions conf/base.config
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Expand Up @@ -74,6 +74,9 @@ process {
cpus = { 24 * task.attempt }
memory = { 30.GB * task.attempt }
}
withName: 'PARABRICKS_FQ2BAM' {
accelerator = { task.executor in ['awsbatch','google-batch','hq','k8s'] ? 4 : null }
}
withName:'CNVKIT_BATCH' {
cpus = { 12 * task.attempt }
memory = { 36.GB * task.attempt }
Expand Down
10 changes: 9 additions & 1 deletion conf/modules/aligner.config
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Expand Up @@ -90,7 +90,15 @@ process {
}

withName: 'PARABRICKS_FQ2BAM' {
ext.args = { "--read-group-id-prefix ${meta.sample_lane_id} --read-group-sm ${meta.patient}_${meta.sample} --read-group-lb ${meta.sample} --read-group-pl ${params.seq_platform}" }
ext.args = { [
// Using specific read group tags for mutect compability
"--read-group-id-prefix ${meta.sample_lane_id}",
"--read-group-sm ${meta.patient}_${meta.sample}",
"--read-group-lb ${meta.sample}",
"--read-group-pl ${params.seq_platform}",
// Using -B 3 for tumor samples
meta.status == 1 ? "--bwa-options='-K 100000000 -Y -B 3'" : "--bwa-options='-K 100000000 -Y'",
].join(' ').trim() }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/preprocessing/parabricks/${meta.id}/" },
Expand Down
73 changes: 37 additions & 36 deletions conf/modules/prepare_genome.config
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Expand Up @@ -18,7 +18,7 @@ process {
// BBSPLIT
withName: '.*:PREPARE_GENOME:BBMAP_BBSPLIT' {
ext.args = 'build=1'
publishDir = [
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference" },
pattern: "bbmap",
Expand All @@ -27,8 +27,9 @@ process {
}

withName: 'BWAMEM1_INDEX' {
ext.when = { !params.bwa && params.step == "mapping" && (params.aligner == "bwa-mem" || params.aligner == "sentieon-bwamem" || params.aligner == "parabricks")}
publishDir = [
ext.when = { !params.bwa && params.step == "mapping" && (params.aligner == "bwa-mem" || params.aligner == "sentieon-bwamem" || params.aligner == "parabricks")}
ext.prefix = { params.aligner == "parabricks" ? "${fasta.name}" : "${fasta.baseName}" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference" },
pattern: "bwa",
Expand All @@ -37,8 +38,8 @@ process {
}

withName: 'BWAMEM2_INDEX' {
ext.when = { !params.bwamem2 && params.step == "mapping" && params.aligner == "bwa-mem2" }
publishDir = [
ext.when = { !params.bwamem2 && params.step == "mapping" && params.aligner == "bwa-mem2" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference" },
pattern: "bwamem2",
Expand All @@ -47,8 +48,8 @@ process {
}

withName: 'CNVKIT_ANTITARGET' {
ext.when = { params.tools && params.tools.split(',').contains('cnvkit') }
publishDir = [
ext.when = { params.tools && params.tools.split(',').contains('cnvkit') }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference" },
pattern: "*{bed}",
Expand All @@ -57,9 +58,9 @@ process {
}

withName: 'CNVKIT_REFERENCE' {
ext.prefix = { 'cnvkit' }
ext.when = { params.tools && params.tools.split(',').contains('cnvkit') && !params.cnvkit_reference }
publishDir = [
ext.prefix = { 'cnvkit' }
ext.when = { params.tools && params.tools.split(',').contains('cnvkit') && !params.cnvkit_reference }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference" },
pattern: "*{cnn}",
Expand All @@ -68,7 +69,7 @@ process {
}

withName: 'DRAGMAP_HASHTABLE' {
ext.when = { !params.dragmap && params.step == "mapping" && params.aligner == "dragmap" }
ext.when = { !params.dragmap && params.step == "mapping" && params.aligner == "dragmap" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference" },
Expand All @@ -79,8 +80,8 @@ process {

withName: 'GATK4_CREATESEQUENCEDICTIONARY' {
// Prevents dict creation, when step is annotate, controlfreec, or when msisensor2 (as the only tool) is run from variantcalling entrystep
ext.when = { !params.dict && params.step != "annotate" && params.step != "controlfreec" && !(params.step == "variantcalling" && params.tools.split(',').size() == 1 && params.tools.contains('msisensor2')) }
publishDir = [
ext.when = { !params.dict && params.step != "annotate" && params.step != "controlfreec" && !(params.step == "variantcalling" && params.tools.split(',').size() == 1 && params.tools.contains('msisensor2')) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/dict" },
pattern: "*dict",
Expand All @@ -89,7 +90,7 @@ process {
}

withName: 'MSISENSOR2_SCAN' {
publishDir = [
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/msisensor2" },
pattern: "*scan",
Expand All @@ -98,7 +99,7 @@ process {
}

withName: 'MSISENSORPRO_SCAN' {
publishDir = [
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/msisensorpro" },
pattern: "*list",
Expand All @@ -107,8 +108,8 @@ process {
}

withName: 'SAMTOOLS_FAIDX' {
ext.when = { !params.fasta_fai && params.step != "annotate" }
publishDir = [
ext.when = { !params.fasta_fai && params.step != "annotate" }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/fai" },
pattern: "*fai",
Expand All @@ -117,8 +118,8 @@ process {
}

withName: 'TABIX_BCFTOOLS_ANNOTATIONS' {
ext.when = { !params.bcftools_annotations_tbi && params.bcftools_annotations && params.tools && params.tools.split(',').contains('bcfann') }
publishDir = [
ext.when = { !params.bcftools_annotations_tbi && params.bcftools_annotations && params.tools && params.tools.split(',').contains('bcfann') }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/bcfann" },
pattern: "*vcf.gz.tbi",
Expand All @@ -127,8 +128,8 @@ process {
}

withName: 'TABIX_DBSNP' {
ext.when = { !params.dbsnp_tbi && params.dbsnp && ((params.step == "mapping" || params.step == "markduplicates" || params.step == "prepare_recalibration") || params.tools && (params.tools.split(',').contains('controlfreec') || params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') || params.tools.split(',').contains('sentieon_dnascope') || params.tools.split(',').contains('muse') || params.tools.split(',').contains('mutect2'))) }
publishDir = [
ext.when = { !params.dbsnp_tbi && params.dbsnp && ((params.step == "mapping" || params.step == "markduplicates" || params.step == "prepare_recalibration") || params.tools && (params.tools.split(',').contains('controlfreec') || params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') || params.tools.split(',').contains('sentieon_dnascope') || params.tools.split(',').contains('muse') || params.tools.split(',').contains('mutect2'))) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/dbsnp" },
pattern: "*vcf.gz.tbi",
Expand All @@ -137,8 +138,8 @@ process {
}

withName: 'TABIX_GERMLINE_RESOURCE' {
ext.when = { !params.germline_resource_tbi && params.germline_resource && params.tools && params.tools.split(',').contains('mutect2') }
publishDir = [
ext.when = { !params.germline_resource_tbi && params.germline_resource && params.tools && params.tools.split(',').contains('mutect2') }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/germline_resource" },
pattern: "*vcf.gz.tbi",
Expand All @@ -147,8 +148,8 @@ process {
}

withName: 'TABIX_KNOWN_INDELS' {
ext.when = { !params.known_indels_tbi && params.known_indels && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && (params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') || params.tools.split(',').contains('sentieon_dnascope'))) ) }
publishDir = [
ext.when = { !params.known_indels_tbi && params.known_indels && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && (params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') || params.tools.split(',').contains('sentieon_dnascope'))) ) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/known_indels" },
pattern: "*vcf.gz.tbi",
Expand All @@ -157,8 +158,8 @@ process {
}

withName: 'TABIX_KNOWN_SNPS' {
ext.when = { !params.known_snps_tbi && params.known_snps && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && (params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') )) ) }
publishDir = [
ext.when = { !params.known_snps_tbi && params.known_snps && (params.step == 'mapping' || params.step == "markduplicates" || params.step == 'prepare_recalibration' || (params.tools && (params.tools.split(',').contains('haplotypecaller') || params.tools.split(',').contains('sentieon_haplotyper') )) ) }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/known_snps" },
pattern: "*vcf.gz.tbi",
Expand All @@ -167,8 +168,8 @@ process {
}

withName: 'TABIX_PON' {
ext.when = { !params.pon_tbi && params.pon && params.tools && params.tools.split(',').contains('mutect2') }
publishDir = [
ext.when = { !params.pon_tbi && params.pon && params.tools && params.tools.split(',').contains('mutect2') }
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/pon" },
pattern: "*vcf.gz.tbi",
Expand All @@ -177,25 +178,25 @@ process {
}

withName: 'UNZIP_ALLELES|UNZIP_LOCI|UNZIP_GC|UNZIP_RT' {
ext.when = { params.tools && params.tools.split(',').contains('ascat')}
publishDir = [
ext.when = { params.tools && params.tools.split(',').contains('ascat')}
publishDir = [
enabled: false
]
}

withName: 'UNTAR_CHR_DIR' {
ext.prefix = 'chr_dir'
ext.when = { params.tools && params.tools.split(',').contains('controlfreec')}
publishDir = [
ext.prefix = 'chr_dir'
ext.when = { params.tools && params.tools.split(',').contains('controlfreec')}
publishDir = [
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/" },
saveAs: { (params.save_reference || params.build_only_index) && !it.equals('versions.yml') ? it : null }
]
}

withName: 'UNTAR_MSISENSOR2_MODELS' {
ext.prefix = 'models'
publishDir = [
ext.prefix = 'models'
publishDir = [
enabled: true,
mode: params.publish_dir_mode,
path: { "${params.outdir}/reference/msisensor2" },
Expand Down
15 changes: 13 additions & 2 deletions conf/test.config
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Expand Up @@ -77,7 +77,18 @@ process {
ext.args = { "--info-key CNN_1D --indel-tranche 0" }
}

withName: 'NFCORE_SAREK:SAREK:FASTQ_PREPROCESS_PARABRICKS:PARABRICKS_FQ2BAM' {
ext.args = { "--read-group-id-prefix ${meta.sample_lane_id} --read-group-sm ${meta.patient}_${meta.sample} --read-group-lb ${meta.sample} --read-group-pl ${params.seq_platform} --low-memory" }
withName: '.*:PARABRICKS_FQ2BAM' {
accelerator = { task.executor in ['awsbatch','google-batch','hq','k8s'] ? 1 : null }
ext.args = { [
// Using specific read group tags for mutect compability
"--read-group-id-prefix ${meta.sample_lane_id}",
"--read-group-sm ${meta.patient}_${meta.sample}",
"--read-group-lb ${meta.sample}",
"--read-group-pl ${params.seq_platform}",
// Using -B 3 for tumor samples
meta.status == 1 ? "--bwa-options='-K 100000000 -Y -B 3'" : "--bwa-options='-K 100000000 -Y'",
// Use low memory mode for tests
"--low-memory",
].join(' ').trim() }
}
}
13 changes: 13 additions & 0 deletions conf/test_full.config
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Expand Up @@ -23,3 +23,16 @@ params {
intervals = 's3://ngi-igenomes/test-data/sarek/S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed'
wes = true
}

process {
// Request a GPU for every parabricks process
// NOTE https://docs.nvidia.com/clara/parabricks/latest/gettingstarted.html#hardware-requirements
withName: 'PARABRICKS_.*' {
cpus = { 48 * task.attempt }
memory = { task.attempt > 1 ? '370.GB' : '186.GB' }
time = { 1.h * task.attempt }
resourceLimits = [cpus: 96, memory: 370.GB]
maxRetries = 3
errorStrategy = { task.exitStatus in [1,2,143,137,104,134,139,255] ? 'retry' : 'finish' }
}
}
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