nf-core/seqsubmit

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nf-core pipeline for data submission to ENA

Stars: 18
Forks: 8
Open beginner issues: 0
Indexed issues: 19

Dominant language: Nextflow
License: MIT
Last GitHub push: Jul 31, 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

19 open issues indexed

metaT assemblies submisison Open

assembly_submit enhancement

Difficulty 3/5 1-2 days Newbie friendliness 55/100

nf-core/seqsubmit#100 · Opened Sep 15, 2026
Pipeline should support long-read submissions end-to-end Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 42/100

nf-core/seqsubmit#98 · Opened Aug 28, 2026
Refactoring of FIND_CONCATENATE usage: replace with collectFile() operator Open

enhancement

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

nf-core/seqsubmit#97 · Opened Aug 27, 2026
Support submission of MAGs/bins generated from co-assemblies Open

enhancement genome_submit

Difficulty 4/5 3-5 days Newbie friendliness 68/100

nf-core/seqsubmit#96 · Opened Aug 27, 2026
Make the test suite runnable without maintainer credentials Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 76/100

nf-core/seqsubmit#95 · Opened Aug 27, 2026
Non-mandatory feilds support Open

enhancement

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

nf-core/seqsubmit#89 · Opened Jul 23, 2026
Submission of a MAG/bin without submitting the assembly or raw reads Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 38/100

nf-core/seqsubmit#87 · Opened Jul 10, 2026
Add tests for --is_private flag for different kinds of data Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 55/100

nf-core/seqsubmit#80 · Opened Jul 2, 2026
Add READS assigned_accessions table into multiqc.report Open

enhancement read_submit

Difficulty 4/5 3-5 days Newbie friendliness 68/100

nf-core/seqsubmit#70 · Opened Jun 4, 2026
Add ENA_VALIDATE_CREDENTIALS module Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 55/100

nf-core/seqsubmit#65 · Opened May 13, 2026
Add viral sequence submission support Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 52/100

nf-core/seqsubmit#63 · Opened May 7, 2026
Support submission of metagenomic assemblies generated from co-assemblies Open

assembly_submit enhancement

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

nf-core/seqsubmit#61 · 1 comment · Opened May 6, 2026
Improve --centre_name and --upload_tpa arguments usage Open

assembly_submit enhancement genome_submit

nf-core/seqsubmit#57 · 1 assignee · Opened Apr 29, 2026
Implement chunking Open

enhancement

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

nf-core/seqsubmit#55 · Opened Apr 24, 2026
Add human contamination removal optional step Open

enhancement

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

nf-core/seqsubmit#51 · Opened Apr 15, 2026
Add eukaryotic MAGs/bins support Open

enhancement eukaryotes

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

nf-core/seqsubmit#40 · Opened Mar 19, 2026
Accept assembly submissions for raw-reads not submitted to ENA Open

assembly_submit enhancement

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

nf-core/seqsubmit#29 · Opened Feb 19, 2026
Write a nf-core/mag samplesheet generator for nf-core/seqsubmit Open

enhancement

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

nf-core/seqsubmit#6 · Opened Oct 24, 2025
Write nf-test for ena-webin-cli Open

enhancement

nf-core/seqsubmit#5 · 1 assignee · Opened Oct 24, 2025

nf-core/seqsubmit

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