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[Bug]: Config parsing failed - Unexpected input ':' in modules.config with Nextflow 26.04.3

bugSomething isn't workingSomething isn't working

Status: Open.

#2207 In nf-core/sarek;

· tommasoregoli opened on Jun 9, 2026

Bug: ConfigParseException in SENTIEON_DEDUP due to undeclared variable (Nextflow 24.10.0+)

bugSomething isn't workingSomething isn't working

Status: Open.

#2206 In nf-core/sarek;

· tommasoregoli opened on Jun 9, 2026

Incorrect VCF file paths in the automatically generated samplesheet

bugSomething isn't workingSomething isn't working

Status: Open.

#2204 In nf-core/sarek;

· DHelix opened on Jun 8, 2026

GATKGenotypeGVCFs step takes ages

bugSomething isn't workingSomething isn't working

Status: Open.

#2202 In nf-core/sarek;

· smhaider opened on Jun 8, 2026

Samplesheet validation issue for --step annotate

bugSomething isn't workingSomething isn't working

Status: Open.

#2201 In nf-core/sarek;

· DHelix opened on Jun 7, 2026

Sarek Concatenate VCF option doesn't concatenate output VCFs.

bugSomething isn't workingSomething isn't working

Status: Open.

#2200 In nf-core/sarek;

· cvillaman opened on Jun 1, 2026

Reference GATK.GRCh37 not working

bugSomething isn't workingSomething isn't working

Status: Open.

#2195 In nf-core/sarek;

· blaker42 opened on May 27, 2026

Parabrics BQSR runs without .tbi indexes (known_sites_indels_tbi not passed to PARABRICKS_FQ2BAM)

bugSomething isn't workingSomething isn't working

Status: Open.

#2193 In nf-core/sarek;

· yambirj opened on May 26, 2026

MSIsensorPro output file name mismatch?

Status: Open.

#2192 In nf-core/sarek;

· DHelix opened on May 24, 2026

FilterMutectCalls --stats parameter

Status: Open.

#2191 In nf-core/sarek;

· DHelix opened on May 24, 2026

SnpEff VCF containing an unexpected warning line

bugSomething isn't workingSomething isn't working

Status: Open.

#2185 In nf-core/sarek;

· albamasmalavila opened on May 18, 2026

Cannot start from --step recalibrate from bam , even though documentation says we can.

bugSomething isn't workingSomething isn't working

Status: Open.

#2183 In nf-core/sarek;

· sicotteh opened on May 12, 2026