Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / nextflow-io/nextflow issues and pull requests

#3435 - Add support for custom conda channels

Pull Request - State: closed - Opened by pditommaso almost 2 years ago
Labels: env/conda

#3422 - Nextflow fails to detect failures due to Failed Node

Issue - State: open - Opened by diego-rt almost 2 years ago - 2 comments
Labels: platform/slurm, stale

#3392 - add support for mpijobs via kubeflow operator

Pull Request - State: open - Opened by xhejtman almost 2 years ago - 23 comments
Labels: executor/k8s

#3385 - Nextflow hanging with still processes to run

Issue - State: open - Opened by diego-rt almost 2 years ago - 2 comments
Labels: stale

#3378 - Operator `collect` breaks when provided with a closure and using pipe syntax

Issue - State: open - Opened by robsyme almost 2 years ago - 14 comments
Labels: kind/bug, lang/operators

#3372 - Validation of published outputs

Issue - State: open - Opened by robsyme almost 2 years ago - 4 comments
Labels: storage/aws-s3, priority

#3367 - Charliecloud and shared cacheDir

Issue - State: open - Opened by l-modolo almost 2 years ago - 14 comments
Labels: stale

#3340 - New command/option to download containers for offline usage

Issue - State: open - Opened by drpatelh about 2 years ago - 9 comments
Labels: wishlist, pinned

#3335 - Nextflow in Docker but with sibling task containers

Issue - State: open - Opened by bentsherman about 2 years ago - 16 comments
Labels: kind/docs, stale, env/docker

#3313 - Support for MPI jobs

Issue - State: open - Opened by xhejtman about 2 years ago - 16 comments
Labels: platform/k8s

#3270 - Catch error: Offline, missing plugin

Issue - State: closed - Opened by ewels about 2 years ago - 3 comments
Labels: triage/not-reproducible, plugins, error-improvements

#3216 - splitFastq produces wrong number of outputs

Issue - State: open - Opened by qscacheri about 2 years ago - 4 comments
Labels: lang/operators

#3196 - Convert docs to Markdown

Pull Request - State: closed - Opened by bentsherman about 2 years ago - 33 comments
Labels: kind/docs

#3124 - Nextflow kuberun login -v volume:/data gives bearer error

Issue - State: closed - Opened by mikarinneoracle about 2 years ago - 4 comments
Labels: platform/k8s, stale

#3121 - Support s3 paths with spacing in nxf_s3_download method

Issue - State: open - Opened by pjongeneel about 2 years ago - 22 comments
Labels: storage/aws-s3, stale

#3045 - Add support for Chinese cloud providers

Issue - State: closed - Opened by bentsherman over 2 years ago - 9 comments
Labels: help wanted

#3027 - Add request/limit for `cpus` directive

Pull Request - State: open - Opened by bentsherman over 2 years ago - 12 comments
Labels: platform/k8s

#3014 - Missing documentation information about poolSize / -pool-size

Issue - State: closed - Opened by mribeirodantas over 2 years ago - 12 comments
Labels: kind/docs

#3013 - sge executor runs on local in nextflow 22.04.04

Issue - State: open - Opened by campanam over 2 years ago - 4 comments
Labels: kind/docs, stale, lang/config

#2978 - pbspro executor - bad qstat usage

Issue - State: open - Opened by xhejtman over 2 years ago - 3 comments
Labels: platform/pbspro, stale

#2966 - process.executor is not recognized for certain nextflow versions and process orders in the configs

Issue - State: closed - Opened by replikation over 2 years ago - 11 comments
Labels: known issue, pinned, lang/config

#2911 - Add resourceLimits directive

Pull Request - State: open - Opened by bentsherman over 2 years ago
Labels: lang/processes

#2893 - Nullable input/output paths

Pull Request - State: open - Opened by jorgeaguileraseqera over 2 years ago - 18 comments
Labels: lang/processes

#2870 - Allow the concurrent run of multiple pipeline revisions

Issue - State: open - Opened by pditommaso over 2 years ago - 34 comments
Labels: priority, software/git

#2857 - Include groovy-cli into dependencies

Issue - State: closed - Opened by ssadedin over 2 years ago - 4 comments

#2773 - Incorporate K8s best practices guide into K8s docs

Issue - State: open - Opened by bentsherman over 2 years ago - 2 comments
Labels: kind/docs, platform/k8s

#2739 - Convert Nextflow docs to markdown

Issue - State: closed - Opened by bentsherman over 2 years ago - 13 comments
Labels: kind/docs

#2695 - Nextflow - SLURM job interface disconnect

Issue - State: open - Opened by nickhsmith over 2 years ago - 18 comments
Labels: executor/slurm

#2693 - Nextflow not terminating after all tasks completed

Issue - State: open - Opened by mebbert over 2 years ago - 11 comments
Labels: triage/not-reproducible

#2678 - DSL2 - emit tuples with optional values

Issue - State: open - Opened by rcannood over 2 years ago - 4 comments
Labels: pinned, lang/processes

#2672 - No task.exitStatus or errorStrategy for SLURM node failure of preemptible nodes on GCP

Issue - State: closed - Opened by davidhbrann over 2 years ago - 12 comments
Labels: executor/slurm, stale

#2622 - [New Feature] Evaluate Closure for every input file

Pull Request - State: open - Opened by Lehmann-Fabian almost 3 years ago - 5 comments
Labels: lang/processes

#2516 - Add support for CPU millis for cpus directive

Pull Request - State: open - Opened by pditommaso almost 3 years ago - 16 comments
Labels: platform/k8s

#2428 - Pod in Failed state, but Nextflow still waiting

Issue - State: closed - Opened by mes5k about 3 years ago - 3 comments
Labels: platform/k8s

#2422 - process.ext set with withName overrides configuration of all processes

Issue - State: open - Opened by grst about 3 years ago - 8 comments
Labels: known issue, lang/config

#2364 - Task .command.log not saved by k8s executor

Issue - State: open - Opened by bentsherman about 3 years ago - 4 comments
Labels: platform/k8s

#2348 - Singularity uses python libraries outside container

Issue - State: open - Opened by grst about 3 years ago - 16 comments
Labels: stale, env/singularity

#2266 - nextflow uses default service account to launch pod in k8s cluster instead of nextflow service account

Issue - State: closed - Opened by MrHassanMurtaza about 3 years ago - 19 comments
Labels: platform/k8s

#2234 - DAG output does not include channel name for multiMap

Issue - State: open - Opened by GordianDziwis over 3 years ago - 1 comment

#2059 - task.workDir is null

Issue - State: closed - Opened by birnbera over 3 years ago - 2 comments
Labels: triage/invalid

#1966 - Use of input repeaters ("each") in DSL2

Issue - State: open - Opened by birnbera over 3 years ago - 3 comments
Labels: bug, lang/processes

#1805 - Resource documentation 1787

Pull Request - State: open - Opened by ewallace almost 4 years ago
Labels: kind/docs

#1726 - Limit rate of queries from Channel.fromSRA() method.

Issue - State: closed - Opened by dstrib about 4 years ago - 2 comments
Labels: stale, lang/operators

#1702 - Passing variable as argument for groupTuple()

Issue - State: closed - Opened by iferres about 4 years ago - 12 comments
Labels: stale, lang/operators

#1670 - Project currently is stuck on revision xxx when using -latest flag

Issue - State: open - Opened by marcadella over 4 years ago - 13 comments
Labels: pinned, software/git

#1544 - Nextflow can't open cache DB error

Issue - State: closed - Opened by ranijames over 4 years ago - 10 comments

#1515 - Output params file

Issue - State: open - Opened by JoseEspinosa over 4 years ago - 16 comments

#1489 - Optional order for publishDir.

Issue - State: open - Opened by srynobio over 4 years ago - 6 comments

#1477 - Job array for more efficient SGE cluster management

Issue - State: open - Opened by mgandal almost 5 years ago - 42 comments
Labels: platform/lsf, platform/sge, platform/slurm, pinned

#1459 - squeue status cannot be fetched

Issue - State: closed - Opened by peter-yufan-zeng almost 5 years ago - 8 comments
Labels: platform/slurm, stale

#1065 - Unify cached processes across workflows

Issue - State: closed - Opened by olgabot over 5 years ago - 5 comments

#1052 - Value of Nextflow channel evaluates to null

Issue - State: closed - Opened by PhilPalmer over 5 years ago - 2 comments

#1045 - Grid executor reports invalid queue status

Issue - State: closed - Opened by pinin4fjords over 5 years ago - 26 comments
Labels: kind/bug

#969 - Singleton list conversion cause quirk behaviour

Issue - State: open - Opened by apeltzer almost 6 years ago - 8 comments
Labels: stale, lang/processes

#942 - different workdir for native groovy code in process

Issue - State: closed - Opened by monfortm almost 6 years ago - 8 comments
Labels: known issue, stale

#903 - Execution metadata tracking and routing

Issue - State: open - Opened by micans about 6 years ago - 37 comments
Labels: kind/feature, nfhack18, pinned

#796 - Allow groupTuple operator to handle multi-size tuples

Issue - State: closed - Opened by micans over 6 years ago - 22 comments
Labels: kind/enhancement, lang/operators

#725 - Error message control

Issue - State: open - Opened by shaze over 6 years ago - 14 comments
Labels: lang/processes

#556 - GNU command line interface

Issue - State: open - Opened by pditommaso almost 7 years ago - 26 comments
Labels: pri/low, kind/enhancement, pinned

#540 - Process prolog and epilog

Issue - State: open - Opened by pditommaso almost 7 years ago - 21 comments
Labels: pinned

#361 - nextflow hanging with slurm executor

Issue - State: closed - Opened by msmootsgi over 7 years ago - 10 comments