nf-core/sarek

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Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

Stars: 603
Forks: 548
Open beginner issues: 0
Indexed issues: 257
Avg merge: 2d 18h
Merged PRs (30d): 1

Dominant language: Nextflow
License: MIT
Last GitHub push: Aug 12, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: help wanted good first issue

Beginner friendly Everything

Open All

257 open issues indexed

GATK4_GATHERPILEUPSUMMARIES concatenates scattered pileup tables out of genome order Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 58/100

nf-core/sarek#2281 · Opened Aug 31, 2026
BAM_MARKDUPLICATES emits duplicate alignment channel under -stub Open

Difficulty 2/5 1-3 hours Newbie friendliness 82/100

nf-core/sarek#2280 · Opened Aug 31, 2026
fgbio GroupReadsByUmi crashes due to missing MQ tag Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 42/100

nf-core/sarek#2279 · Opened Aug 27, 2026
ControlFreec pipeline does not run Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 42/100

nf-core/sarek#2278 · 2 comments · Opened Aug 25, 2026
Generated `variantcalled.csv` from Strelka Sarek run rejected for anotation step with vep Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 64/100

nf-core/sarek#2276 · Opened Aug 25, 2026
no_intervals = true conflicts with aligner = parabricks Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/sarek#2274 · Opened Aug 19, 2026
CNVkit and TIDDIT process only the first sample when multiple samples share a calling category Open

Difficulty 3/5 1-2 days Newbie friendliness 72/100

nf-core/sarek#2273 · Opened Aug 19, 2026
Support gVCF output and joint germline calling for Parabricks HaplotypeCaller Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 42/100

nf-core/sarek#2261 · 1 comment · Opened Aug 7, 2026
Sentieon doesn't work when using Seqera Platform and a license server Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 48/100

nf-core/sarek#2256 · 3 comments · Opened Aug 3, 2026
bwa-mem2.avx2 crashes (SIGSEGV) on Intel Core Ultra (Arrow Lake) under WSL2 — workaround: force SSE4.2 binary Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 42/100

nf-core/sarek#2254 · 1 comment · Opened Jul 31, 2026
Somatic tumor-normal run with indexcov fails at SAMTOOLS_REINDEX_BAM due to tuple mismatch Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 55/100

nf-core/sarek#2251 · Opened Jul 28, 2026
Add GATK like filtering to Parabricks Haplotypecaller path Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/sarek#2250 · Opened Jul 28, 2026
varlociraptor error during "MERGE_GERMLINE_SOMATIC_VCFS" Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

nf-core/sarek#2231 · 2 comments · Opened Jul 13, 2026
varlociraptor custom scenario parameter issue Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/sarek#2230 · 2 comments · Opened Jul 10, 2026
Reuse of intervals-files Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

nf-core/sarek#2226 · 1 comment · Opened Jul 1, 2026
MUSE channel cardinality Open

Difficulty 2/5 1-3 hours Newbie friendliness 72/100

nf-core/sarek#2224 · Opened Jun 29, 2026
Update vars to secrets in awsmegatest action Open

Difficulty 2/5 1-3 hours Newbie friendliness 56/100

nf-core/sarek#2223 · Opened Jun 29, 2026
Allow bam output for parabricks path Open

Difficulty 3/5 1-2 days Newbie friendliness 68/100

nf-core/sarek#2222 · Opened Jun 29, 2026
Tech Debt: Consolidate = vs set usage Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

nf-core/sarek#2212 · Opened Jun 15, 2026
Incorrect VCF file paths in the automatically generated samplesheet Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 48/100

nf-core/sarek#2204 · Opened Jun 8, 2026
Samplesheet validation issue for --step annotate Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 48/100

nf-core/sarek#2201 · 3 comments · Opened Jun 7, 2026
Sarek Concatenate VCF option doesn't concatenate output VCFs. Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 48/100

nf-core/sarek#2200 · Opened Jun 1, 2026
Reference GATK.GRCh37 not working Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 52/100

nf-core/sarek#2195 · Opened May 27, 2026
Parabrics BQSR runs without .tbi indexes (known_sites_indels_tbi not passed to PARABRICKS_FQ2BAM) Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 64/100

nf-core/sarek#2193 · Opened May 26, 2026
MSIsensorPro output file name mismatch? Open

Difficulty 2/5 1-3 hours Newbie friendliness 75/100

nf-core/sarek#2192 · 1 comment · Opened May 24, 2026
FilterMutectCalls --stats parameter Open

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

nf-core/sarek#2191 · 3 comments · Opened May 24, 2026
SnpEff VCF containing an unexpected warning line Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/sarek#2185 · 1 comment · Opened May 18, 2026
Cannot start from --step recalibrate from bam , even though documentation says we can. Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/sarek#2183 · 1 comment · Opened May 12, 2026
ASCAT gets genomeVersion = "NULL" with manual refs / --igenomes_ignore unless --ascat_genome is set Open

Difficulty 4/5 3-5 days Newbie friendliness 48/100

nf-core/sarek#2182 · Opened May 8, 2026
Jobs failing during CNVKIT_BATCH Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/sarek#2163 · 3 comments · Opened Mar 30, 2026
Error Manta WGS Open

bug moreinfo

Difficulty 3/5 1-2 days Newbie friendliness 30/100

nf-core/sarek#2158 · 1 comment · Opened Mar 18, 2026
CRAM corruption and unexpected behavior when a BGZIP-compressed reference is used Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/sarek#2157 · Opened Mar 18, 2026
Automatic ASCAT reference file generation for WES Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

nf-core/sarek#2155 · Opened Mar 12, 2026
vep plugin for mastermind missing adding vep_extra file in main.nf Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 48/100

nf-core/sarek#2150 · Opened Feb 26, 2026
Enable CombineGVCFs if no intervals are provided as fallback to GenomicsDB Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/sarek#2145 · Opened Feb 23, 2026
Constant OOM error for GetPileupSummaries on EC2 Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/sarek#2140 · Opened Feb 12, 2026
OOM error for GetPileupSummaries on EC2 Open

question

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/sarek#2131 · 2 comments · Opened Feb 10, 2026
Strelka2 stuck at 99% for over 24 hours (reopen) Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

nf-core/sarek#2127 · 4 comments · Opened Feb 7, 2026
UMI-aware Sarek Open

question

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/sarek#2114 · 10 comments · Opened Jan 28, 2026
Join mismatch error Open

moreinfo

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/sarek#2110 · 2 comments · Opened Jan 20, 2026
GATK BaseRecalibrator interval usage affects variant calling Open

question

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/sarek#2097 · 4 comments · Opened Jan 14, 2026
Enhance tests/variantcalling_all with all tools Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

nf-core/sarek#2090 · Opened Jan 12, 2026
ASCAT Exome processing steps incorrect for hg38 Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

nf-core/sarek#2089 · Opened Jan 8, 2026
Question: Advanced filtering with --bcftools_filter_criteria parameter Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

nf-core/sarek#2085 · 1 comment · Opened Dec 18, 2025
Prepare reference before run pipeline Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/sarek#2072 · 3 comments · Opened Dec 9, 2025
Inquiry about integrating Octopus variant caller into Sarek Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/sarek#2056 · 1 comment · Opened Nov 17, 2025
How to skip rerunning tasks that have already been completed when using the -resume parameter? Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 25/100

nf-core/sarek#2042 · 4 comments · Opened Oct 30, 2025
401 Unauthorized error from Singularity gatk Open

question

Difficulty 4/5 3-5 days Newbie friendliness 30/100

nf-core/sarek#2040 · 5 comments · Opened Oct 23, 2025
Bug Report — Join mismatch when using mutect2 tool Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/sarek#2036 · 2 comments · Opened Oct 21, 2025
No automatic email recieved after successful completion of pipeline in Sarek ver. 3.6.0 Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/sarek#2034 · 5 comments · Opened Oct 17, 2025

nf-core/sarek

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