Deprecations
This page lists Nextflow features that are discouraged, deprecated, or recently removed. Use it to find out what you need to change before a feature goes away.
- Discouraged features still work, but better alternatives are available. They may be deprecated in the future.
- Deprecated features still work, but will be removed in a future release.
- Removed features are no longer supported. Migrate away from them before upgrading your Nextflow version.
See Migration notes for the full list of changes in each release.
Discouraged
| Feature | Alternative |
|---|---|
kuberun command | Launch with Fusion |
| Using params outside the entry workflow | Explicit inputs |
Legacy parameter declarations (params.foo = ...) | params block |
Workflow | and & operators | Method calls and assignments |
.out to access process/workflow outputs | Assignments |
| Legacy operators | Core operators |
Process when section | Conditional logic in the calling workflow |
| Using global variables in a process | Process inputs |
publishDir directive | Workflow outputs |
Deprecated
Language
| Feature | Deprecated | Replacement |
|---|---|---|
Channel.from() | 19.10 | channel.of() or channel.fromList() |
file process input and output qualifier | 19.10 | path |
baseDir | 20.04 | projectDir |
addParams and params clauses in include declarations | 24.10 | Explicit inputs |
Process shell section | 25.04 | Process script section |
Channel to access channel factories | 25.10 | channel |
Legacy syntax parser (NXF_SYNTAX_PARSER=v1) | 26.04 | Strict syntax |
channel.fromSRA() | 26.04 | Entrez Direct |
Process directives
| Feature | Deprecated | Replacement |
|---|---|---|
storeDir | 26.10 | Explicit workflow logic |
Configuration
| Feature | Deprecated | Replacement |
|---|---|---|
aws.client.uploadStorageClass | 23.10 | aws.client.storageClass |
https://api.tower.nf as the Seqera Platform endpoint | 24.04 | https://api.cloud.seqera.io |
manifest.author | 24.10 | manifest.contributors |
| Workflow handlers in config files | 25.10 | Trace observer in a plugin |
manifest.defaultBranch | 26.04 | Automatic detection of the default branch |
seqera.executor.autoLabels | 26.10 | tower.autoLabels |
Command line
| Feature | Deprecated | Replacement |
|---|---|---|
Named workflow entry (-entry) | 24.10 | Params in the entry workflow |
Feature flags and environment variables
| Feature | Deprecated | Replacement |
|---|---|---|
NXF_CONTAINER_ENTRYPOINT_OVERRIDE | 22.10 | None |
nextflow.enable.dsl and NXF_DEFAULT_DSL | 25.04 | None (DSL2 is the only DSL) |
nextflow.enable.configProcessNamesValidation | 25.10 | Strict syntax |
nextflow.enable.strict and NXF_ENABLE_STRICT | 26.04 | Strict syntax |
Google Batch machine type selection via Cloud Info, and NXF_CLOUDINFO_ENABLED | 26.10 | machineType directive |
Removed
| Feature | Deprecated | Removed | Replacement |
|---|---|---|---|
| DSL1 | 22.04 | 23.04 | DSL2 |
docker.userEmulation | 24.04 | None | |
Glacier auto-retrieval (aws.client.glacierAutoRetrieval) | 24.04 | Restore objects with the AWS CLI | |
@Grab annotation | 24.10 | Plugins | |
| Spack support in Wave | 24.10 | 25.04 | Conda |
google-lifesciences executor | 24.10 | 25.10 | google-batch |
aws.client.protocol, signerOverride, socketRecvBufferSizeHint, socketSendBufferSizeHint, and userAgent | 25.10 | None | |
aws.client.uploadChunkSize, uploadMaxAttempts, uploadMaxThreads, and uploadRetrySleep | 25.10 | aws.client.minimumPartSize and aws.client.multipartThreshold | |
-with-weblog option of run | 25.04 | 26.10 | nf-weblog plugin |
echo directive | 22.04 | 26.10 | debug |