frattalab/rna_seq_snakemake

Snakemake Pipeline For RNA-Seq in UCL Cluster

Stars: 10
Forks: 5
Open beginner issues: 0
Indexed issues: 8

Dominant language: Python
License: No license data
Last GitHub push: Aug 5, 2026
Latest indexed: Sep 16, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: No beginner labels indexed
PR merge metrics: No merged PRs in 30d

Beginner friendly Everything

Open All

8 open issues indexed

conda instead of mamba Open

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

frattalab/rna_seq_snakemake#57 · Opened Mar 6, 2024
DESEQ2 snakemake rule runs every comparison in the comparisons.yaml everytime it runs Open

frattalab/rna_seq_snakemake#56 · 1 assignee · Opened Jan 23, 2023
use of conda has us approaching file limits Open

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

frattalab/rna_seq_snakemake#55 · 2 comments · Opened Jan 18, 2023
Refine minimal QC modules and reporting Open

frattalab/rna_seq_snakemake#38 · 1 assignee · Opened Apr 19, 2022
Move to snakemake profiles for cluster submission and job logs to main output dir not submissions Open

low priority

frattalab/rna_seq_snakemake#30 · 1 assignee · Opened Jun 25, 2021
Test data bundled with repo to cover all permutations Open

frattalab/rna_seq_snakemake#27 · 2 comments · 1 assignee · Opened Jun 24, 2021
Option to create (strand-specific) coverage bigwigs Open

enhancement low priority

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

frattalab/rna_seq_snakemake#14 · 1 comment · Opened Jan 14, 2021
Make schema for sample_table.csv to try and catch layout errors Open

enhancement low priority

frattalab/rna_seq_snakemake#8 · 1 assignee · Opened Oct 22, 2020

A short digest of beginner-friendly GitHub issues.