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remove access to params in twistcgp.nf

Status: Open.

#111 In fulcrumgenomics/twistcgp;

· znorgaard opened on Jun 10, 2026

Bump pinned picard/markduplicates SHA to pick up stub .bai fix

Status: Open.

#101 In fulcrumgenomics/twistcgp;

· znorgaard opened on Apr 28, 2026

Bare boolean flags rejected by nf-schema 2.5.1 (e.g. --use_msisensor_pro_licensed)

Status: Open.

#100 In fulcrumgenomics/twistcgp;

· znorgaard opened on Apr 28, 2026

ALIGNBAM stub references bwa but container ships bwa-mem2

Status: Open.

#99 In fulcrumgenomics/twistcgp;

· znorgaard opened on Apr 28, 2026

Allow more custom annotation files for VEP annotation

Status: Open.

#97 In fulcrumgenomics/twistcgp;

· RSWilson1 opened on Apr 28, 2026

Feature request - accept tar.gz files for VEP cache

Status: Open.

#96 In fulcrumgenomics/twistcgp;

· RSWilson1 opened on Apr 28, 2026

Possible bug when running in cloud

bugSomething isn't workingSomething isn't working

Status: Open.

#95 In fulcrumgenomics/twistcgp;

· RSWilson1 opened on Apr 28, 2026

Q: Does the twistcgp pipeline support lane-split FASTQs (multiple FASTQ pairs per sample) via the samplesheet?

Status: Open.

#92 In fulcrumgenomics/twistcgp;

· RSWilson1 opened on Apr 23, 2026

MSIsensorPro requires a baseline file not the output of scan.

Status: Open.

Bug

#91 In fulcrumgenomics/twistcgp;

· RSWilson1 opened on Apr 14, 2026

adopt something close to nf-core's nf-test approach

Status: Open.

#86 In fulcrumgenomics/twistcgp;

· znorgaard opened on Mar 19, 2026

improve msisensor2 model provenance

Status: Open.

#61 In fulcrumgenomics/twistcgp;

· znorgaard opened on Sep 24, 2025

bump to snpeff 5.3

Status: Open.

#57 In fulcrumgenomics/twistcgp;

· znorgaard opened on Sep 12, 2025