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output-records: prove output-tree parity with dev on every route, in CI and on S3/Azure

Status: Open.

#1952 In nf-core/rnaseq;

· pinin4fjords opened on Sep 24, 2026

output-records: finish the publishDir cutover (live >> per target, samplesheet index, deletion pass, cleanups)

Status: Open.

#1949 In nf-core/rnaseq;

· pinin4fjords opened on Sep 24, 2026

output-records: restore the dev output tree (FQ_LINT names, RustQC layout, reference indexes)

Status: Open.

#1946 In nf-core/rnaseq;

· pinin4fjords opened on Sep 24, 2026

with_umi: transcriptome-side samtools stats silently collide with genome-side (config include order bug)

Status: Open.

#1941 In nf-core/rnaseq;

· pinin4fjords opened on Sep 24, 2026

HISAT2 alignments bypass --min_mapped_reads filtering

Status: Open.

#1940 In nf-core/rnaseq;

· pinin4fjords opened on Sep 24, 2026

Workflow outputs, phase 3: static types for the record boundaries

Status: Open.

#1935 In nf-core/rnaseq;

· pinin4fjords opened on Sep 23, 2026

Workflow outputs, phase 2: replace publishDir with publish: / output {}

Status: Open.

#1934 In nf-core/rnaseq;

· pinin4fjords opened on Sep 23, 2026

Workflow outputs, phase 1: emit per-sample result records from every stage

Status: Open.

#1933 In nf-core/rnaseq;

· pinin4fjords opened on Sep 23, 2026

Migrate to Nextflow workflow outputs via per-stage result records (tracking issue)

Status: Open.

#1931 In nf-core/rnaseq;

· pinin4fjords opened on Sep 23, 2026

Adopt the docker_arm/singularity_arm container-config profile scheme, retire conf/arm.config

Status: Open.

#1920 In nf-core/rnaseq;

· pinin4fjords opened on Sep 16, 2026

Reorganise usage docs with a user-centric structure

documentation

Status: Open.

#1737 In nf-core/rnaseq;

· pinin4fjords opened on Feb 27, 2026

More than 1 reference genome

enhancement

Status: Open.

#1695 In nf-core/rnaseq;

· gfill88 opened on Feb 9, 2026