nextflow-io/nextflow issues and pull requests

#5401 - Change to scan.allowedLevels

Pull Request - State: closed - Opened by pditommaso 22 days ago - 1 comment

#5400 - Add Google LS deprecation notice

Pull Request - State: closed - Opened by pditommaso 22 days ago - 1 comment

#5399 - Add more out formats to config command

Pull Request - State: closed - Opened by pditommaso 24 days ago - 1 comment

#5398 - Accept config from YAML/JSON

Issue - State: open - Opened by bskubi 24 days ago - 3 comments

#5397 - Mitigate Interrupted system call on trace_file writes

Pull Request - State: open - Opened by infinite-turtles 25 days ago - 1 comment

#5396 - Consider exposing trace record meta info in the task context

Issue - State: open - Opened by pditommaso 25 days ago - 2 comments

#5395 - Enable AWS secrets manager

Pull Request - State: open - Opened by pditommaso 25 days ago - 1 comment

#5394 - Consolidate resolve stub run logic

Pull Request - State: closed - Opened by pditommaso 25 days ago - 1 comment

#5392 - Add wave docs

Pull Request - State: closed - Opened by pditommaso 26 days ago - 3 comments

#5391 - AWS: switch from containerProperties to ecsProperties

Pull Request - State: open - Opened by tom-seqera 26 days ago - 1 comment

#5390 - Provide google storage object as input to -params-file

Issue - State: open - Opened by peter-fsdx 26 days ago

#5389 - Add retry policy in Channel.fromSRA factory

Pull Request - State: closed - Opened by jorgee 26 days ago - 1 comment

#5388 - Include retry policy in Channel.fromSRA factory

Pull Request - State: closed - Opened by jorgee 26 days ago - 1 comment

#5387 - Include retry policy in Channel.fromSRA factory

Pull Request - State: closed - Opened by jorgee 26 days ago - 4 comments

#5386 - Life after Nextflow+Apache Ignite. Alternatives?

Issue - State: closed - Opened by dgarrimar 27 days ago - 1 comment

#5384 - Add support for Wave container status API

Pull Request - State: closed - Opened by pditommaso 27 days ago - 3 comments
Labels: software/wave

#5382 - Run Deepvariant docker inside nextflow

Issue - State: closed - Opened by dbhayal9 28 days ago

#5380 - AWSBatch -- CgroupError: Agent could not create task's platform resources

Issue - State: closed - Opened by mozack 28 days ago - 1 comment

#5379 - Remove unused reportsOpts

Pull Request - State: closed - Opened by pditommaso 28 days ago - 1 comment

#5377 - Include rateLimit to the Channel.fromSRA factory

Pull Request - State: closed - Opened by jorgee 29 days ago - 4 comments

#5376 - Passing a quoted string starting with `-` to nextflow CLI has unexpected behaviour

Issue - State: open - Opened by cjw85 29 days ago - 1 comment

#5375 - Identify default git branch when downloading pipelines (#3593)

Pull Request - State: closed - Opened by tom-seqera 29 days ago - 2 comments
Labels: software/git

#5374 - Access to previous task used resources for resources optimization

Issue - State: closed - Opened by luisas 29 days ago - 14 comments

#5373 - Cleanup directive does not work when `bucket-dir` is specified.

Issue - State: open - Opened by siddharthab about 1 month ago - 5 comments

#5372 - Support accelerator optimized VMs in Google Cloud

Issue - State: open - Opened by siddharthab about 1 month ago - 1 comment
Labels: executor/google-batch

#5371 - Workflow publish directive for channels can not take empty relative path

Issue - State: open - Opened by siddharthab about 1 month ago - 3 comments

#5368 - Increase in PutLogEvents for cloud watch due to batch job

Issue - State: closed - Opened by lacoak21 about 1 month ago - 1 comment
Labels: executor/aws-batch

#5367 - Failed to pull singularity image?

Issue - State: closed - Opened by zenmck about 1 month ago - 2 comments

#5366 - Fix workflow onComplete and onError in the entry workflow

Pull Request - State: open - Opened by bentsherman about 1 month ago - 1 comment

#5365 - Fix incorrect total count at the end of the execution

Pull Request - State: closed - Opened by jorgee about 1 month ago - 2 comments

#5364 - Separate the store directory from the filename in the trace, dag, report, and timeline scopes

Issue - State: open - Opened by mahesh-panchal about 1 month ago
Labels: lang/config

#5363 - nextflow 24.0.4.4 never exit due to incomplete file transfer

Issue - State: open - Opened by divinomas-gh about 1 month ago - 4 comments

#5362 - Harmonise documentation for hybrid cloud execution

Pull Request - State: open - Opened by adamrtalbot about 1 month ago - 1 comment
Labels: docs

#5361 - Add hybrid workflow documentation for Azure

Pull Request - State: closed - Opened by adamrtalbot about 1 month ago - 4 comments
Labels: docs

#5360 - FIxedInputStream raises false error when reading only part of a file

Issue - State: open - Opened by bentsherman about 1 month ago - 1 comment
Labels: bug

#5359 - Fixing issue when retrying with stub

Pull Request - State: closed - Opened by jorgee about 1 month ago - 4 comments

#5358 - Hybrid execution does not work on Azure

Issue - State: closed - Opened by adamrtalbot about 1 month ago - 5 comments
Labels: bug, executor/azure-batch

#5356 - Add retry policy to google batch describe task

Pull Request - State: closed - Opened by bentsherman about 1 month ago - 1 comment
Labels: executor/google-batch

#5354 - Operator `subscribe` returns wrong results when chained and hangs at the end

Issue - State: open - Opened by siddharthab about 1 month ago - 1 comment
Labels: lang/operators

#5353 - Support including existing files within watchPath?

Issue - State: open - Opened by siddharthab about 1 month ago - 5 comments
Labels: lang/operators

#5352 - Use `Channel` instead of `channel`

Pull Request - State: open - Opened by bentsherman about 1 month ago - 8 comments
Labels: docs

#5351 - Hash improvements

Pull Request - State: open - Opened by bentsherman about 1 month ago - 7 comments
Labels: cache-breaking

#5350 - Azure Batch executor does not always respect error strategy

Issue - State: open - Opened by raylim about 1 month ago - 3 comments
Labels: executor/azure-batch

#5349 - fromFilePairs 'flat' still includes the grouping key (misunderstanding of the documentation)

Issue - State: closed - Opened by Gullumluvl about 1 month ago - 5 comments
Labels: lang/operators

#5348 - Manage moduleBinaries feature flag in the pipeline script

Pull Request - State: closed - Opened by jorgee about 1 month ago - 2 comments

#5347 - Ability to publish to S3 buckets with Object Lock by including md5 checksum.

Issue - State: open - Opened by robsyme about 1 month ago - 2 comments
Labels: storage/aws

#5345 - Detecting errors in data unstaging

Pull Request - State: open - Opened by jorgee about 1 month ago - 1 comment

#5343 - Failure in stub causes nextflow to run the script-section?

Issue - State: closed - Opened by oyvinev about 1 month ago - 4 comments
Labels: lang/processes

#5336 - Document formal script syntax

Pull Request - State: open - Opened by bentsherman about 1 month ago - 6 comments
Labels: docs

#5332 - Slurm oom-kill due to memory is ignored.

Issue - State: open - Opened by oliverdrechsel about 1 month ago

#5331 - Fix AWS spot attempts with zero value

Pull Request - State: closed - Opened by pditommaso about 1 month ago - 1 comment
Labels: backport/24.04.5

#5330 - AWS MaxSpotAttempts set to zero it is not respected on versions prior to 24.08.0-edge

Issue - State: closed - Opened by jordeu about 1 month ago - 1 comment
Labels: bug

#5329 - Add Java 23 support

Pull Request - State: closed - Opened by pditommaso about 1 month ago - 1 comment

#5328 - Fix Azure Fusion env misses credentials when no key or SAS provided

Pull Request - State: closed - Opened by pditommaso about 1 month ago - 2 comments

#5327 - publishDir pattern '{".bam", "len.txt"}' is not publishing the output files

Issue - State: open - Opened by kemin711 about 1 month ago - 2 comments

#5326 - Fix e2e trigger event on PR

Pull Request - State: closed - Opened by pditommaso about 1 month ago - 2 comments

#5325 - Update docs secrets

Pull Request - State: closed - Opened by christopher-hakkaart about 1 month ago - 3 comments

#5324 - singularity.cacheDir does not work properly with containers that have ':' in the filename

Issue - State: open - Opened by stevekm about 1 month ago - 2 comments
Labels: software/singularity

#5323 - Change behavior of `process.cpus` back to `--cpus` when using Docker with a local executor

Issue - State: open - Opened by mriffle about 1 month ago - 5 comments
Labels: software/docker

#5322 - Add `manifest.contributors` config option

Pull Request - State: open - Opened by bentsherman about 1 month ago - 6 comments
Labels: lang/config

#5321 - Unable to run a private github repository with a private submodule

Issue - State: open - Opened by mark-gerarts about 1 month ago - 3 comments
Labels: software/git

#5320 - E2E are not triggered in a pull request

Issue - State: closed - Opened by pditommaso about 1 month ago - 4 comments

#5319 - Is there a way to find out the requested entry point (cli option -entry) from within main.nf

Issue - State: closed - Opened by vruano about 1 month ago - 2 comments

#5318 - Include tower prefix in Batch job names

Pull Request - State: closed - Opened by jorgee about 2 months ago - 10 comments

#5316 - config.md - mention string or map

Pull Request - State: closed - Opened by ewels about 2 months ago - 2 comments
Labels: docs

#5315 - Prefix AWS Batch jobs with Workflow ID

Issue - State: open - Opened by pditommaso about 2 months ago
Labels: executor/aws-batch

#5314 - Include additional fields to manifest

Pull Request - State: closed - Opened by jorgee about 2 months ago - 12 comments
Labels: lang/config

#5313 - Workflow 'publish:' feature and optional processes

Issue - State: open - Opened by maressyl about 2 months ago - 1 comment

#5312 - Using AWS secrets in `includeConfig` doesn't work

Issue - State: open - Opened by bentsherman about 2 months ago - 2 comments
Labels: plugins, lang/config

#5311 - Improve Logs on optional outputs in process

Issue - State: closed - Opened by jfouret about 2 months ago - 2 comments

#5310 - Different Singularity behaviours between 22.10.7 vs 23.04.0+

Issue - State: open - Opened by HarryHung about 2 months ago - 8 comments

#5309 - envWhitelist not working with `docker.sudo = true`

Issue - State: open - Opened by fntlnz about 2 months ago - 5 comments
Labels: software/docker

#5308 - Feature request - custom caching strategy

Issue - State: open - Opened by robsyme about 2 months ago - 6 comments

#5307 - Resume a partially done pipeline starts from the beginning.

Issue - State: open - Opened by kemin711 about 2 months ago

#5306 - Overriding `resourceLimits`

Issue - State: open - Opened by mirpedrol about 2 months ago - 2 comments
Labels: lang/config

#5304 - Improve Wave build timeout handling

Pull Request - State: closed - Opened by pditommaso about 2 months ago - 1 comment

#5303 - Bump groovy 4.0.23

Pull Request - State: closed - Opened by pditommaso about 2 months ago - 1 comment

#5302 - Fix large mermaid diagrams

Pull Request - State: closed - Opened by bentsherman about 2 months ago - 1 comment

#5301 - HTML DAG gives syntax error in text

Issue - State: closed - Opened by gregorysprenger about 2 months ago - 1 comment

#5300 - Update container handling with charliecloud

Pull Request - State: closed - Opened by nschan about 2 months ago - 7 comments

#5299 - Add container tip in the task error report

Pull Request - State: closed - Opened by pditommaso about 2 months ago - 1 comment

#5298 - SLURM jobs being set as RUNNING when the actual state of the job is failed

Issue - State: open - Opened by sgopalan98 about 2 months ago - 3 comments

#5296 - Test platform

Pull Request - State: closed - Opened by pditommaso about 2 months ago - 1 comment

#5295 - `NXF_FILE_ROOT` not properly resolved for relative paths

Issue - State: open - Opened by artur-baranowski-aa about 2 months ago - 4 comments
Labels: wontfix

#5294 - Add Fusion version pinning info to Fusion config scope

Pull Request - State: closed - Opened by llewellyn-sl about 2 months ago - 1 comment
Labels: docs, storage/fusion

#5293 - Fix failOnIgnore causes task monitor to stop submitting tasks

Pull Request - State: open - Opened by bentsherman about 2 months ago - 1 comment

#5291 - Workflow option `failOnIgnore` causes workflow to hang

Issue - State: open - Opened by kgalens about 2 months ago - 4 comments

#5289 - Auto-casting behaviour of Strings to file/Path objects differs between relative and absolute paths

Issue - State: closed - Opened by robsyme 2 months ago - 4 comments
Labels: wontfix

#5288 - moduleBinaries in toplevel module/projectDir not found, (sharp edge)

Issue - State: open - Opened by feiloo 2 months ago - 2 comments

#5287 - fix: Azure Fusion env misses credentials when no key or SAS provided

Pull Request - State: closed - Opened by adamrtalbot 2 months ago - 21 comments

#5286 - Azure storage authentication errors in 24.08.0-edge with Fusion enabled

Issue - State: open - Opened by alberto-miranda 2 months ago

#5285 - `nextflow run` from GitHub fails to override default parameters with command line arguments

Issue - State: closed - Opened by alexdhill 2 months ago - 2 comments
Labels: wontfix

#5281 - Fix job array syntax for PBS/Torque executor

Pull Request - State: closed - Opened by bentsherman 2 months ago - 2 comments
Labels: executor/pbs

#5280 - `pull` and `run` treat Github usernames as case sensitive on Linux

Issue - State: open - Opened by harper357 2 months ago - 3 comments
Labels: wontfix, software/git

#5279 - In Google Batch, add missed warning

Pull Request - State: closed - Opened by siddharthab 2 months ago - 3 comments
Labels: executor/google-batch

#5278 - Support Azure Managed Identities in Fusion configuration logic

Pull Request - State: closed - Opened by alberto-miranda 2 months ago - 1 comment
Labels: storage/azure, storage/fusion

#5277 - Setting dumpHashes=false in nextflow.config is still taking it as true since version 23

Issue - State: closed - Opened by pavan-kotha-strandls 2 months ago - 2 comments

#5276 - Nextflow failing to detect task exit/failure due to slurm failed node

Issue - State: open - Opened by sereeena 2 months ago
Labels: executor/slurm

#5275 - Fix http corrupted download

Pull Request - State: closed - Opened by pditommaso 2 months ago - 6 comments
Labels: backport/24.04.5

#5274 - [Docs] Workflow output: Include `publish` in example.

Pull Request - State: closed - Opened by ewels 2 months ago - 2 comments
Labels: docs

GitHub / nextflow-io/nextflow issues and pull requests