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nextflow-io

12 indexed repositories · View on GitHub

nextflow
A DSL for data-driven computational pipelines

Groovy · 3488 stars
training
Nextflow training material

Nextflow · 271 stars
nf-schema
Functionality for working with pipeline and sample sheet schema files in Nextflow pipelines

Groovy · 57 stars
vscode-language-nextflow
Nextflow language support for Visual Studio Editor

TypeScript · 38 stars
language-server
The Nextflow language server

Java · 31 stars
nf-co2footprint
A Nextflow plugin to estimate the CO₂ footprint of pipeline runs.

Groovy · 29 stars
nf-weblog
Implement weblog plugin for Nextflow

Groovy · 10 stars
website
Nextflow public web site

HTML · 9 stars
nf-ga4gh
GA4GH plugin for Nextflow

Java · 6 stars
tree-sitter-nextflow

JavaScript · 4 stars
schemas
Specifications of Nextflow schemas

Shell · 4 stars
nf-trino

HTML · 0 stars

Beginner friendly Everything

Open All

Typed-conversion code lens silently drops comments Open

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

nextflow-io/language-server#182 · 1 comment · Opened Sep 18, 2026
nf-tower: interactive auth prompts hang or fail when stdin is not a terminal Open

Difficulty 3/5 1-2 days Newbie friendliness 74/100

nextflow-io/nextflow#7642 · Opened Sep 18, 2026
nextflow 26.04.x+ incompatible with LSF 10.1.0, Stopping a head job fails to stop compute jobs. Open

executor/lsf triage/investigate

Difficulty 3/5 1-2 days Newbie friendliness 68/100

nextflow-io/nextflow#7640 · 1 comment · Opened Sep 18, 2026
Globstar output patterns may result in invalid move operations when `scratch = true` and `stageOutMode = move` Open

triage/investigate

Difficulty 3/5 1-2 days Newbie friendliness 58/100

nextflow-io/nextflow#7637 · Opened Sep 18, 2026
Google Batch: share a single getTaskStatus lookup in getTraceRecord() Open

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

nextflow-io/nextflow#7636 · Opened Sep 17, 2026
can't write output index files using google-batch executor & gs storage bucket for output dir Open

storage/gcp triage/investigate

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

nextflow-io/nextflow#7633 · Opened Sep 17, 2026
Google Batch: Fusion scratch mount omitted for machines with built-in Local SSDs (-lssd) Open

Difficulty 3/5 1-2 days Newbie friendliness 74/100

nextflow-io/nextflow#7627 · Opened Sep 15, 2026
Feature request: periodic progress logging during samplesheet validation Open

enhancement

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

nextflow-io/nf-schema#224 · 2 comments · Opened Sep 15, 2026
Reference to `-resume` flag in the wrong place Open

Difficulty 1/5 Under an hour Newbie friendliness 92/100

nextflow-io/training#991 · Opened Sep 14, 2026
Translation pipeline can write invalid/corrupted output when updating against an existing translation (duplicate frontmatter, leaked LLM preamble, broken YAML) Open

Difficulty 3/5 1-2 days Newbie friendliness 78/100

nextflow-io/training#985 · Opened Sep 13, 2026
Basic architecture awareness when using singularity/apptainer - container image name Open

Difficulty 4/5 3-5 days Newbie friendliness 50/100

nextflow-io/nextflow#7617 · Opened Sep 13, 2026
Basic architecture awareness when using singularity/apptainer - pulling Open

Difficulty 3/5 1-2 days Newbie friendliness 68/100

nextflow-io/nextflow#7616 · 1 comment · Opened Sep 13, 2026
Hello Nextflow workflow image Open

hello series

nextflow-io/training#978 · 2 comments · 1 assignee · Opened Sep 4, 2026
Local executor: IllegalThreadStateException in LocalTaskHandler.checkIfCompleted hard-aborts the whole session instead of just the affected task Open

triage/investigate

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

nextflow-io/nextflow#7569 · Opened Sep 1, 2026
Workflow outputs don't work as expected with an early teturn Open

triage/investigate

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

nextflow-io/nextflow#7537 · 1 comment · Opened Aug 24, 2026
PBSPro executor spamming PBS server with requests Open

executor/pbs executor/pbspro

Difficulty 2/5 1-3 hours Newbie friendliness 78/100

nextflow-io/nextflow#7535 · 3 reactions · Opened Aug 24, 2026
splitCsv / CsvParser does not support RFC 4180 escaped quotes Open

Difficulty 2/5 1-3 hours Newbie friendliness 84/100

nextflow-io/nextflow#7529 · Opened Aug 22, 2026
AWS Batch: expose the job-termination rate limit as real config instead of reusing executor.submitRateLimit (and an internal pool name) Open

executor/aws-batch

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

nextflow-io/nextflow#7502 · 1 comment · Opened Aug 18, 2026
nf-azure: support Microsoft Fabric OneLake as object storage Open

storage/azure

Difficulty 5/5 Over a week Newbie friendliness 45/100

nextflow-io/nextflow#7495 · Opened Aug 17, 2026
Output globs descend into hidden directories, collecting Fusion's internal .fusion/ metadata as task outputs Open

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

nextflow-io/nextflow#7480 · 2 comments · Opened Aug 14, 2026
Add configurable retry with cooldown for failed URL file staging Open

Difficulty 5/5 Over a week Newbie friendliness 48/100

nextflow-io/nextflow#7475 · Opened Aug 13, 2026
Add a rename method for records Open

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

nextflow-io/nextflow#7473 · Opened Aug 12, 2026
Profiles via includeConfig are not applied in command line order Open

lang/config

Difficulty 3/5 1-2 days Newbie friendliness 62/100

nextflow-io/nextflow#7472 · Opened Aug 12, 2026
Workspace scan is deferred behind the debounce, so early cross-file requests see an almost-empty AST cache Open

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

nextflow-io/language-server#175 · 1 comment · Opened Aug 9, 2026
ci: automate registry and GitHub releases from one tag Open

Difficulty 4/5 3-5 days Newbie friendliness 62/100

nextflow-io/nf-trino#12 · Opened Aug 8, 2026
fix: support or remove documented JDBC connection properties Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nextflow-io/nf-trino#11 · Opened Aug 8, 2026
docs: align testing guidance with actual test tiers Open

Difficulty 3/5 1-2 days Newbie friendliness 72/100

nextflow-io/nf-trino#10 · Opened Aug 8, 2026
test: make runnable fixtures fail closed Open

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

nextflow-io/nf-trino#9 · Opened Aug 8, 2026
fix: import the SQL extension from nf-trino Open

Difficulty 3/5 1-2 days Newbie friendliness 72/100

nextflow-io/nf-trino#8 · Opened Aug 8, 2026
cloudcache.enabled does not properly enable/disable usage of the nf-cloudcache plugin Open

triage/investigate

Difficulty 3/5 1-2 days Newbie friendliness 72/100

nextflow-io/nextflow#7456 · Opened Aug 7, 2026
maxForks slot is leaked when TaskHandler.submit() throws Open

bug triage/investigate

Difficulty 3/5 1-2 days Newbie friendliness 72/100

nextflow-io/nextflow#7447 · Opened Aug 5, 2026
Container resolution errors bypass errorStrategy, silently downgrading `finish` to `terminate` Open

bug triage/investigate

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

nextflow-io/nextflow#7446 · Opened Aug 5, 2026
Run hangs forever in Session.await() when a shutdown callback blocks during abort Open

bug triage/investigate

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

nextflow-io/nextflow#7444 · 1 comment · Opened Aug 5, 2026
Legacy Groovy style typing is silently ignored Open

triage/investigate

Difficulty 3/5 1-2 days Newbie friendliness 52/100

nextflow-io/nextflow#7438 · 4 comments · Opened Aug 4, 2026
Allow groupBy for records with a specific key Open

lang/dataflow

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

nextflow-io/nextflow#7422 · 7 comments · Opened Jul 31, 2026
Bad cancelation for cache db Open

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

nextflow-io/nextflow#7421 · 3 comments · Opened Jul 31, 2026
-stub before another option (not directly before the pipeline arg) resolves wrong pipeline (nextflow-io/true) Open

triage/investigate

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

nextflow-io/nextflow#7419 · 1 comment · Opened Jul 31, 2026
Boolean parameter validation failure in nf-core/rnaseq 3.26.0 with Nextflow 26.04 Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nextflow-io/nextflow#7411 · 1 comment · 1 reaction · Opened Jul 30, 2026
`record.subMap` can return either a `RecordMap` or a `LinkedHashMap` depending on key input Open

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

nextflow-io/nextflow#7406 · 1 comment · Opened Jul 28, 2026
subMap not recognized as a valid method for record types Open

Difficulty 3/5 1-2 days Newbie friendliness 68/100

nextflow-io/language-server#169 · Opened Jul 28, 2026
A `params` block makes pipe-form operators undefined in the entry workflow Open

bug triage/investigate

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

nextflow-io/nextflow#7399 · Opened Jul 28, 2026
Directories fail to publish via `>>` operator in cloud environments Open

storage/gcp triage/investigate

Difficulty 3/5 1-2 days Newbie friendliness 78/100

nextflow-io/nextflow#7398 · 1 comment · Opened Jul 28, 2026
Misleading error message when using shadowed process name in map Open

triage/investigate

Difficulty 3/5 1-2 days Newbie friendliness 48/100

nextflow-io/nextflow#7397 · 1 comment · Opened Jul 28, 2026
Feature request: per-process Spot → on-demand fallback for Google Batch Open

Difficulty 4/5 3-5 days Newbie friendliness 58/100

nextflow-io/nextflow#7396 · 1 reaction · Opened Jul 27, 2026
Feature request: literal type Open

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

nextflow-io/nextflow#7392 · 2 comments · Opened Jul 27, 2026
Allow config scope aliases (e.g. objectStorage for aws) Open

lang/config

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

nextflow-io/nextflow#7387 · Opened Jul 26, 2026
K8s: disrupted pods with condition DisruptionTarget consume the retry budget Open

executor/k8s

Difficulty 3/5 1-2 days Newbie friendliness 72/100

nextflow-io/nextflow#7378 · 1 comment · Opened Jul 24, 2026
Static typing: false 'Argument … is not compatible' warning on process→process record wiring (cross-file check ordering) Open

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

nextflow-io/language-server#165 · Opened Jul 23, 2026
[Feature]: Add CI timeline to provenance file Open

💎 enhancement

nextflow-io/nf-co2footprint#414 · 1 assignee · Opened Jul 22, 2026
CI: measure parse-rate and show a coverage badge in the README Open

enhancement

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

nextflow-io/tree-sitter-nextflow#30 · Opened Jul 15, 2026

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