nf-core/denovotranscript

A pipeline for de novo transcriptome assembly of paired-end short reads from bulk RNA-seq

Stars: 26
Forks: 3
Open beginner issues: 0
Indexed issues: 7

Dominant language: Nextflow
License: MIT
Last GitHub push: Jul 27, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

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7 open issues indexed

Busco TypeError: only 0-dimensional arrays can be converted to Python scalars Open

bug

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

nf-core/denovotranscript#54 · Opened May 6, 2026
Duplicated error with soft_filtered_transcripts is true Open

bug

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

nf-core/denovotranscript#52 · Opened Dec 29, 2025
Separate assemblies for separate samples Open

enhancement

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

nf-core/denovotranscript#48 · 1 comment · 3 reactions · Opened Oct 7, 2025
SPAdes / Trinity running out of space still Open

bug

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

nf-core/denovotranscript#41 · 1 comment · Opened Apr 8, 2025
JSON schema: Denovotranscript Open

documentation

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

nf-core/denovotranscript#40 · Opened Mar 25, 2025
Consider splitting Trinity stages into separate tasks Open

enhancement

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

nf-core/denovotranscript#39 · Opened Feb 11, 2025
Using Trinity with grid_exec Open

bug

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

nf-core/denovotranscript#38 · 2 comments · 1 reaction · Opened Jan 31, 2025

A short digest of beginner-friendly GitHub issues.