nextflow-io/nextflow

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A DSL for data-driven computational pipelines

Stars: 3.5k
Forks: 811
Open beginner issues: 0
Indexed issues: 313
Avg merge: 2d 11h
Merged PRs (30d): 61

Dominant language: Groovy
License: Apache-2.0
Last GitHub push: Sep 18, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: good first issue help wanted

Beginner friendly Everything

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313 open issues indexed

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
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
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
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
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
Google Batch: Setting `accelerator` directive removes docker ENTRYPOINT instructions Open

executor/google-batch software/docker triage/investigate

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

nextflow-io/nextflow#7315 · 1 comment · Opened Jul 9, 2026
Allow a list of keys in the `by` option of the v2 version of the `join` operator Open

lang/dataflow triage/investigate

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

nextflow-io/nextflow#7309 · 4 comments · 1 reaction · Opened Jul 8, 2026
AWS Batch: task polls forever when the job is missing from the DescribeJobs response — no bound, unlike grid's exitReadTimeout Open

triage/investigate

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

nextflow-io/nextflow#7301 · Opened Jul 3, 2026
Docker API Version Open

software/docker

Difficulty 3/5 1-2 days Newbie friendliness 64/100

nextflow-io/nextflow#7253 · Opened Jun 23, 2026
S3ObjectSummaryLookup lists without a delimiter, over-listing sibling prefixes Open

storage/aws

Difficulty 2/5 1-3 hours Newbie friendliness 70/100

nextflow-io/nextflow#7224 · 2 comments · Opened Jun 11, 2026
Process recursion considers topic channels for cardinality of outputs Open

lang/processes

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

nextflow-io/nextflow#7222 · 1 comment · Opened Jun 11, 2026
Support passing multiple values to a single input in nextflow module run Open

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

nextflow-io/nextflow#7212 · 1 comment · Opened Jun 9, 2026
Should `notifyEvent` be dispatched asynchronously? Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

nextflow-io/nextflow#7189 · 1 reaction · Opened May 29, 2026
Allow opting out of foreign-file staging for paths on worker-accessible mounts Open

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

nextflow-io/nextflow#7186 · 3 comments · 7 reactions · Opened May 28, 2026
Feature request: Structured changelog Open

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

nextflow-io/nextflow#7178 · 1 comment · 1 reaction · Opened May 27, 2026
Dependency Dashboard Open

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

nextflow-io/nextflow#7135 · Opened May 13, 2026
Validation using records is not working Open

error-improvements

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

nextflow-io/nextflow#7133 · 1 comment · Opened May 12, 2026
K8S API error resilience Open

executor/k8s

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

nextflow-io/nextflow#7122 · 2 comments · Opened May 8, 2026
Add Jitter to Task Polling Mechanism Open

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

nextflow-io/nextflow#7115 · Opened May 7, 2026
`List` type parameters are incompatible with the CLI Open

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

nextflow-io/nextflow#7099 · 1 comment · 1 reaction · Opened May 5, 2026

nextflow-io/nextflow

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