nextflow-io/nextflow issues and pull requests

#3951 - Failure to execute ch-run with current charliecloud version (0.32).

Issue - State: closed - Opened by t-kreitler over 1 year ago - 4 comments

#3950 - Nextflow loses track of jobs when they are moved to a new LSF queue

Issue - State: open - Opened by chrisamiller over 1 year ago
Labels: platform/lsf

#3949 - Clarify tip about groupTuple size and groupKey

Pull Request - State: closed - Opened by bentsherman over 1 year ago
Labels: kind/docs

#3948 - Google Batch VM issue

Issue - State: open - Opened by Joaodemeirelles over 1 year ago - 2 comments
Labels: platform/google-batch

#3947 - withName config only respected using regex or within profile block

Issue - State: open - Opened by didillysquat over 1 year ago
Labels: lang/config

#3946 - Add CPU model name to trace files and traceRecord

Pull Request - State: open - Opened by skrakau over 1 year ago - 2 comments

#3944 - Missing plugin 'nf-amazon'

Issue - State: closed - Opened by bingli2019 over 1 year ago

#3943 - Unable to start plugin 'nf-amazon' required by s3://ngi-igenomes/igenomes/

Issue - State: closed - Opened by bingli2019 over 1 year ago - 1 comment

#3942 - Add support for custom custom root directory to resolve relative paths

Pull Request - State: closed - Opened by pditommaso over 1 year ago - 3 comments

#3939 - join doesn't match the same keys

Issue - State: open - Opened by berguner over 1 year ago - 1 comment
Labels: lang/operators

#3938 - Fixing bug 2428 for errorStrategy ignore

Pull Request - State: closed - Opened by mes5k over 1 year ago - 1 comment
Labels: platform/k8s

#3937 - Google Batch jobs can be submitted to spot GPUs by default

Issue - State: closed - Opened by ejseqera over 1 year ago - 9 comments
Labels: platform/google-batch

#3936 - queueSize does not work at all, always submit 100 jobs

Issue - State: closed - Opened by zillurbmb51 over 1 year ago - 2 comments
Labels: platform/slurm

#3935 - Better documentation for groupTuple and groupKey

Issue - State: closed - Opened by benbfly over 1 year ago - 2 comments
Labels: kind/docs

#3933 - Walk file tree on directory publish

Pull Request - State: open - Opened by bentsherman over 1 year ago

#3929 - Document use of aws scope for non-Amazon/AWS S3.

Pull Request - State: closed - Opened by jfy133 over 1 year ago - 6 comments
Labels: kind/docs

#3928 - fix: Azure retry policy corrected

Pull Request - State: closed - Opened by adamrtalbot over 1 year ago - 1 comment
Labels: platform/azure-batch

#3927 - Azure jobs correctly deleted after completion

Pull Request - State: closed - Opened by adamrtalbot over 1 year ago - 1 comment
Labels: platform/azure-batch

#3926 - Azure Batch jobs not cleaned up after task failure

Issue - State: closed - Opened by adamrtalbot over 1 year ago - 6 comments
Labels: platform/azure-batch

#3925 - get params-file via workflow object

Issue - State: closed - Opened by mattheatley over 1 year ago - 4 comments

#3923 - Error executing process > 'get_software_versions'

Issue - State: closed - Opened by MinLuke over 1 year ago

#3920 - Update the version of Nextflow used to 23.04.1

Issue - State: closed - Opened by gf-atebbe over 1 year ago

#3918 - Move 'report' stderr to different stream or file?

Issue - State: closed - Opened by MikeWLloyd over 1 year ago - 1 comment

#3917 - QA workflow/script version on report.html

Issue - State: open - Opened by joanmarticarreras over 1 year ago

#3916 - Add/process.dockerfile

Pull Request - State: open - Opened by marcodelapierre over 1 year ago - 5 comments

#3915 - DSL1 warning remains

Issue - State: open - Opened by ewels over 1 year ago
Labels: kind/bug

#3913 - FATAL: container creation failed with singularity profile

Issue - State: closed - Opened by nhhaidee over 1 year ago

#3911 - ERROR - java.nio.file.attribute.BasicWithKeyFileAttributeView

Issue - State: closed - Opened by lescai over 1 year ago - 2 comments

#3910 - connection refused

Issue - State: closed - Opened by Claudio-dur over 1 year ago - 1 comment

#3909 - Task grouping

Pull Request - State: open - Opened by bentsherman over 1 year ago

#3907 - Phil docs version notes

Pull Request - State: closed - Opened by ewels over 1 year ago - 4 comments

#3906 - Enable static compilation for task processing code

Pull Request - State: closed - Opened by bentsherman over 1 year ago - 8 comments

#3905 - Implement job array using TaskRun as carrier

Pull Request - State: open - Opened by pditommaso over 1 year ago - 17 comments

#3904 - Fix problem args were not correctly represented in debug yaml

Pull Request - State: closed - Opened by Lehmann-Fabian over 1 year ago - 1 comment
Labels: platform/k8s

#3903 - Submit jobs in batches to allow easier monitoring

Issue - State: open - Opened by raimondsre over 1 year ago - 1 comment

#3902 - Cleanup version notes in docs

Pull Request - State: closed - Opened by bentsherman over 1 year ago - 6 comments
Labels: kind/docs

#3901 - Support enums in cache helper

Pull Request - State: closed - Opened by bentsherman over 1 year ago - 4 comments

#3900 - add ACCOUNT_NAME and SAS_TOKEN env variables to fusion environment

Pull Request - State: closed - Opened by pabloaledo over 1 year ago - 1 comment
Labels: platform/azure-batch, fusion

#3899 - Caching/resuming does not work with groovy Enums

Issue - State: closed - Opened by nh13 over 1 year ago - 7 comments

#3898 - PR #3338 seems not working well with k8s LimitRange

Issue - State: open - Opened by jacobsin over 1 year ago
Labels: platform/k8s

#3897 - Tentative implementation for task arrays [DRAFT]

Pull Request - State: closed - Opened by pditommaso over 1 year ago - 2 comments

#3895 - README: added link to Spack Environments docs page

Pull Request - State: closed - Opened by marcodelapierre over 1 year ago

#3894 - Missing documentation page?

Issue - State: closed - Opened by marcodelapierre over 1 year ago - 2 comments

#3893 - Specifying fields with Nextflow log command

Issue - State: closed - Opened by georgiesamaha over 1 year ago - 2 comments
Labels: kind/docs

#3892 - Support array jobs

Pull Request - State: open - Opened by bentsherman over 1 year ago - 25 comments
Labels: platform/lsf, platform/sge, platform/aws-batch, platform/slurm, platform/pbs, platform/pbspro

#3890 - Fix Apptainer rendering by removing superflous space.

Pull Request - State: closed - Opened by jfy133 over 1 year ago
Labels: kind/docs

#3884 - Add snake_case to params normalization

Pull Request - State: open - Opened by ahvigil over 1 year ago - 6 comments

#3879 - nextflow "run" and "pull" should do a shallow clone by default

Issue - State: closed - Opened by ahstram over 1 year ago - 1 comment
Labels: git-interaction

#3877 - Add reference in Google section in the docs to the nextflow's blogpost

Pull Request - State: open - Opened by mribeirodantas over 1 year ago
Labels: kind/docs

#3876 - Spack page is unavailable for latest docs

Issue - State: closed - Opened by mribeirodantas over 1 year ago - 1 comment
Labels: kind/docs

#3871 - Preview support for virtual threads

Pull Request - State: closed - Opened by pditommaso over 1 year ago - 5 comments

#3862 - Fair directive - downstream processes stop unexpectedly

Issue - State: open - Opened by jbanusco over 1 year ago - 2 comments
Labels: lang/processes

#3861 - Add disk resource with type option for google batch

Pull Request - State: open - Opened by bentsherman over 1 year ago - 6 comments
Labels: platform/google-batch

#3858 - Tentative solution of unstage exit code

Pull Request - State: closed - Opened by pditommaso over 1 year ago
Labels: wontfix

#3849 - Add `eager` cleanup option

Pull Request - State: open - Opened by bentsherman over 1 year ago - 1 comment

#3847 - Killing Nextflow run does not kill Google Batch VMs

Issue - State: open - Opened by BeyondTheProof over 1 year ago - 16 comments
Labels: platform/google-batch

#3836 - Fix cleanup with remote work dir

Pull Request - State: open - Opened by bentsherman over 1 year ago - 3 comments
Labels: storage/aws-s3, storage/azure, storage/gcp

#3831 - Add an option types to splitCsv() to cast the variable types

Pull Request - State: closed - Opened by mirpedrol over 1 year ago - 25 comments
Labels: lang/operators

#3818 - Add support for temporary output paths

Pull Request - State: open - Opened by bentsherman over 1 year ago - 8 comments
Labels: lang/processes

#3816 - Add process.shell directive documentation

Pull Request - State: closed - Opened by njspix over 1 year ago - 2 comments
Labels: kind/docs

#3802 - Add initial task graph and metadata json file

Pull Request - State: open - Opened by bentsherman over 1 year ago - 5 comments

#3793 - Incorporate DSL2 features into docs

Pull Request - State: open - Opened by bentsherman over 1 year ago - 1 comment
Labels: kind/docs

#3789 - Support accelerator directive for Azure Batch

Issue - State: open - Opened by bentsherman over 1 year ago - 8 comments
Labels: platform/azure-batch

#3788 - Document `nextflow.enable` and `nextflow.preview` feature flags

Pull Request - State: closed - Opened by bentsherman over 1 year ago - 1 comment
Labels: kind/docs

#3786 - Updates to Spack in standard Nextflow

Pull Request - State: closed - Opened by marcodelapierre over 1 year ago - 15 comments

#3784 - Document `-pool-size` run option

Pull Request - State: closed - Opened by bentsherman over 1 year ago - 4 comments
Labels: kind/docs

#3780 - Issue with newer version of groovy-yaml

Issue - State: open - Opened by zachcp over 1 year ago - 8 comments

#3768 - ConcurrentModificationException when using `publishDir`

Issue - State: closed - Opened by robsyme over 1 year ago - 7 comments

#3759 - 3758 - errorStrategy cache issue fix

Pull Request - State: open - Opened by mhrvol over 1 year ago - 1 comment

#3754 - Safe guard when using publishDir directive

Issue - State: open - Opened by Phuong-Le over 1 year ago - 6 comments

#3739 - Support maps for combine, join, and groupTuple operators

Pull Request - State: open - Opened by bentsherman over 1 year ago
Labels: lang/operators

#3736 - Add timeout on scheduling wait

Pull Request - State: open - Opened by pditommaso over 1 year ago

#3724 - Add publish operator

Pull Request - State: open - Opened by bentsherman over 1 year ago - 2 comments
Labels: lang/operators

#3712 - Add named arguments for processes and workflows

Pull Request - State: open - Opened by bentsherman over 1 year ago
Labels: lang/processes

#3711 - Validation of task outputs

Issue - State: open - Opened by robsyme over 1 year ago - 5 comments
Labels: storage/aws, pinned

#3706 - Add arity option for path inputs and outputs

Pull Request - State: open - Opened by bentsherman over 1 year ago - 6 comments
Labels: lang/processes

#3701 - Add support for platform architecture and microarchitectures

Issue - State: closed - Opened by pditommaso over 1 year ago - 22 comments

#3697 - Add Fusion support to Condor executor

Pull Request - State: open - Opened by bentsherman over 1 year ago - 2 comments
Labels: platform/htcondor, fusion

#3687 - Support default values for process inputs

Pull Request - State: open - Opened by bentsherman over 1 year ago - 7 comments
Labels: lang/processes

#3671 - Remove deprecated DSL syntax

Pull Request - State: open - Opened by bentsherman over 1 year ago

#3670 - Remove `Channel.from` in favor of `Channel.of`

Pull Request - State: closed - Opened by bentsherman over 1 year ago - 1 comment
Labels: lang/operators

#3664 - Remove deprecated code (part 1)

Pull Request - State: open - Opened by bentsherman over 1 year ago - 1 comment

#3651 - Allow closures in file/url for `trace`,`report`,`timeline`,`dag`,`weblog`

Pull Request - State: open - Opened by fbdtemme over 1 year ago

#3636 - [Beta Test] Wave Containers: add support for the Spack package manager

Pull Request - State: closed - Opened by marcodelapierre over 1 year ago - 57 comments

#3630 - Support instance template in google batch

Pull Request - State: open - Opened by daigok over 1 year ago - 13 comments
Labels: platform/google-batch

#3629 - Add instance template option to google batch

Issue - State: open - Opened by daigok over 1 year ago - 6 comments
Labels: platform/google-batch

#3600 - CLI v2

Pull Request - State: open - Opened by bentsherman almost 2 years ago - 52 comments

#3593 - Main branch not recognised when executing an online workflow

Issue - State: closed - Opened by marcodelapierre almost 2 years ago - 12 comments
Labels: pinned, software/git

#3562 - Upgrade kryo to 5.4.0

Pull Request - State: open - Opened by bentsherman almost 2 years ago - 9 comments
Labels: cache-breaking

#3555 - AWS config refactor using AWS credentials chain

Pull Request - State: closed - Opened by pditommaso almost 2 years ago - 14 comments

#3544 - Use of `Optional` in groovy classes breaks all caching

Issue - State: open - Opened by tfenne almost 2 years ago - 5 comments

#3533 - params resolution for dicts

Issue - State: open - Opened by HalfPhoton almost 2 years ago - 4 comments
Labels: wontfix

#3503 - Use of files in bin folder (third party scripts) on Docker runs

Issue - State: open - Opened by jameswagner almost 2 years ago - 4 comments
Labels: pri/awaiting-more-evidence, stale, env/docker

#3500 - Issue with staged files from s3

Issue - State: open - Opened by maxulysse almost 2 years ago - 8 comments
Labels: storage/aws-s3, stale

#3476 - The value taken by a parameter is affected by uppercase letters in the parameter name

Issue - State: open - Opened by fortune9 almost 2 years ago - 1 comment
Labels: stale, lang/modules

#3460 - Allow to publish timeline, trace and DAG files as a Tower report

Issue - State: open - Opened by jordeu almost 2 years ago - 1 comment
Labels: stale

#3459 - Better migration notes for breaking changes

Issue - State: open - Opened by corneliusroemer almost 2 years ago - 2 comments
Labels: kind/docs, pinned

#3458 - Make docs of previous versions available on readthedocs

Issue - State: open - Opened by corneliusroemer almost 2 years ago - 3 comments
Labels: kind/docs, pinned

#3457 - Include changelog in documentation on readthedocs

Issue - State: open - Opened by corneliusroemer almost 2 years ago - 3 comments
Labels: kind/docs, pinned

#3455 - NXF_DEBUG level is not properly handled

Issue - State: open - Opened by YuxinShi0423 almost 2 years ago - 1 comment
Labels: stale

GitHub / nextflow-io/nextflow issues and pull requests