nf-core/nascent

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Nascent Transcription Processing Pipeline

Stars: 25
Forks: 11
Open beginner issues: 0
Indexed issues: 52

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

Open All

52 open issues indexed

NET-Seq data analysis Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 15/100

nf-core/nascent#217 · Opened Oct 20, 2025
PINTS tasks stall when FASTA includes GL/KI contigs; works after restricting to chr Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 42/100

nf-core/nascent#215 · Opened Jul 18, 2025
Generate comprehensive HTML QC reports with interactive plots Open

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

nf-core/nascent#214 · Opened Jul 13, 2025
Implement eNRSA algorithmic optimizations for speed and memory Open

nf-core/nascent#213 · 1 assignee · Opened Jul 13, 2025
Add NRSA enhancer prioritization and target gene assignment Open

nf-core/nascent#212 · 1 assignee · Opened Jul 13, 2025
Integrate seqOutBias for enzymatic bias correction Open

nf-core/nascent#211 · 1 assignee · Opened Jul 13, 2025
Comprehensive documentation update for enhanced pipeline features Open

documentation

nf-core/nascent#210 · 1 assignee · Opened Jul 13, 2025
Plan integration roadmap for nascent RNA pipeline enhancements Open

nf-core/nascent#209 · 1 assignee · Opened Jul 13, 2025
Implement RNA degradation ratio calculation Open

enhancement high-priority

nf-core/nascent#206 · 1 assignee · Opened Jul 13, 2025
Improve UMI handling and deduplication options Open

enhancement high-priority

nf-core/nascent#205 · 1 assignee · Opened Jul 13, 2025
Add serial alignment preprocessing for contamination removal Open

high-priority

nf-core/nascent#204 · 1 assignee · Opened Jul 13, 2025
Add comprehensive nascent RNA QC metrics module Open

enhancement

nf-core/nascent#203 · 1 assignee · Opened Jul 13, 2025
Add an intervene module Open

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

nf-core/nascent#199 · Opened May 23, 2025
Remove intermediate bams Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

nf-core/nascent#198 · Opened May 23, 2025
Turn off quality checks by default Open

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

nf-core/nascent#197 · Opened May 23, 2025
JSON schema: Nascent Open

documentation

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

nf-core/nascent#192 · Opened Mar 25, 2025
Add license to bin scripts Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

nf-core/nascent#188 · Opened Jan 13, 2025
Add bed2tssbed conversion Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/nascent#187 · Opened Jan 5, 2025
Report number of transcripts identified per method in MultiQC Open

nf-core/nascent#186 · 1 assignee · Opened Dec 25, 2024
Clean up Publishing Open

Difficulty 3/5 1-2 days Newbie friendliness 20/100

nf-core/nascent#176 · Opened Nov 26, 2024
groHMM fails with CHM13 occasionally Open

bug

nf-core/nascent#172 · 1 assignee · Opened Oct 21, 2024
Consider tsshmm Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 15/100

nf-core/nascent#164 · 1 comment · Opened Sep 18, 2024
v.2.2.0 fails on multiple replicates of the same sample Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 25/100

nf-core/nascent#159 · 6 comments · Opened Aug 14, 2024
Sample names must contain at least underscore (?) Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

nf-core/nascent#158 · 1 comment · Opened Aug 14, 2024
Support not pooling reads for HOMER Open

enhancement

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

nf-core/nascent#153 · Opened Aug 3, 2024
Flakey test Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

nf-core/nascent#148 · Opened Jul 22, 2024
Issue with concatenation of technical replicates Open

bug

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

nf-core/nascent#143 · Opened May 7, 2024
Discrepancy between bigwigs generated by bedtools and deeptools Open

bug

nf-core/nascent#123 · 1 comment · 1 assignee · Opened Oct 19, 2023
Test results say chr22 when the ref is chr21? Open

bug

nf-core/nascent#121 · 1 assignee · Opened Sep 27, 2023
Flipped bigwig strands in PROseq samples Open

nf-core/nascent#115 · 3 comments · 1 assignee · Opened Jun 29, 2023
Bedtools sort output isn't deterministic Open

bug

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

nf-core/nascent#102 · Opened Jan 19, 2023
Improve reporting when no transcripts are found Open

enhancement

nf-core/nascent#95 · 1 assignee · Opened Oct 31, 2022
Example of 3D genome integration Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/nascent#93 · Opened Oct 26, 2022
motif production for region Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/nascent#92 · Opened Oct 26, 2022
Example of integration with ATAC-seq pipeline output Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/nascent#91 · Opened Oct 26, 2022
Support STAR Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/nascent#90 · Opened Oct 26, 2022
Clean up published files Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/nascent#89 · Opened Oct 25, 2022
Add plotHeatmap by Gene and by Transcript Open

enhancement

nf-core/nascent#88 · 1 reaction · 1 assignee · Opened Oct 25, 2022
Refactor ext.when Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/nascent#85 · Opened Oct 21, 2022
Migrate CI tests to pytest-workflow Open

enhancement

nf-core/nascent#84 · 1 assignee · Opened Oct 20, 2022
Set up AWS Full tests Open

enhancement

nf-core/nascent#78 · 1 assignee · Opened Oct 17, 2022
Include Homer annotate peaks from chip-seq Open

enhancement

nf-core/nascent#73 · 1 assignee · Opened Oct 4, 2022
Add PINTS Visualizer Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/nascent#72 · Opened Oct 3, 2022
Create Subway pipeline Open

enhancement

nf-core/nascent#68 · 1 assignee · Opened Sep 21, 2022
Refactor Prepare Genome Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 32/100

nf-core/nascent#60 · Opened Sep 12, 2022
GROHMM and CHM13 Open

bug

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

nf-core/nascent#56 · Opened Sep 5, 2022
Add dynseq tracks Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

nf-core/nascent#48 · Opened Jun 6, 2022
Upstream Subworkflows Open

nf-core/nascent#44 · 1 assignee · Opened Apr 4, 2022
Support and benchmark aligners Open

enhancement

nf-core/nascent#41 · 1 assignee · Opened Mar 28, 2022
Test with dREG web submission Open

nf-core/nascent#31 · 1 comment · 1 assignee · Opened Mar 3, 2022

nf-core/nascent

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