nextflow-io/nextflow

splitCsv handles commas incorrectly when cells contain commas within quoted strings 6 days ago

good first issue triage/investigate

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

"Missing project main script" error when there is a directory with the workflow name 13 days ago

error-improvements good first issue triage/investigate

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Nextflow on POSIX breaking on input paths starting with hyphen / dash ('-') 13 days ago

good first issue software/bash triage/investigate

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

A flag to remove quotation marks from index file 13 days ago

stale good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

AWS Batch Fargate requires exact CPU values? 13 days ago

executor/aws-batch good first issue triage/investigate

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Expand `.splitCsv()` to allow comments in CSV and TSV files about 2 months ago

good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Support for AWS Batch Consumable Resources about 2 months ago

executor/aws-batch stale good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Add an option to the file method to check for md5sum 4 months ago

good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Pipeline Info - Timeline - Inconsistent verical alignment (small issue / nit) 4 months ago

good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Devcontainer Support 5 months ago

good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Cumulative job duration (realtime) in the nextflow execution report 6 months ago

stale good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Support shallow clones of submodules 6 months ago

stale software/git good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

How to set the computing resources (cpus, memory) in total submitted jobs 6 months ago

executor/slurm stale good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Extend Task traces with hash codes of retry attempts 6 months ago

stale good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Include workflow and script version in execution report 6 months ago

stale good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Support Gitlab OAuth 2.0 identity provider API 6 months ago

stale software/git good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Support for Pixi 7 months ago

stale good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

nf-test.config should be excluded from linting 7 months ago

good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Conda config option to specify CONDA_SUBDIR environment variable 7 months ago

stale software/conda good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Support reservation when provisioning VM/ accelerators on Google Batch 7 months ago

stale executor/google-batch good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

In summary report, allow breakdowns by sub-workflow for processes 7 months ago

stale good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

In Summary Report Task Table long process names overflow into adjacent cells 8 months ago

stale good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Adding a parameter for AnsiLogObserver delay 8 months ago

good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

COLUMNS environment variable not honored 8 months ago

good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Add an env var which points to a config file for all pipelines 8 months ago

lang/config good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Accelerate SLURM job state queries with --only-job-state option to squeue 8 months ago

executor/slurm good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Custom AWS Batch job names 8 months ago

executor/aws-batch stale good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

moduleBinaries doesn't work with top-level module 8 months ago

bug lang/modules good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Conda: Support `.lock` file extensions. 8 months ago

software/conda good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Support container streaming for Google Batch 8 months ago

executor/google-batch good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Support custom config and params-file in `nextflow config` command 8 months ago

good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Option to disable volume mount optimisation 8 months ago

software/docker good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Improve error message when failures happen due to proxy settings 8 months ago

help wanted error-improvements

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Add error strategy shortcuts 8 months ago

good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Ability to use a time delay in 'errorStrategy' to re-submit scheduler jobs 8 months ago

help wanted

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Allow AWS S3 Access Points 8 months ago

help wanted storage/aws

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

nextflow clone does not clone commit hashes 8 months ago

help wanted software/git

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Error when using Shifter as container runtime in Nextflow >23.08.0-edge 8 months ago

help wanted stale

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

Add hyperlinks to HTML DAG 10 months ago

stale good first issue

nextflow-io/nextflow

3.4K

A DSL for data-driven computational pipelines

Groovy

#aws#bioinformatics#cloud#dataflow#docker#groovy#hello#hpc#nextflow#pipeline#pipeline-framework#reproducible-research#reproducible-science#sge#singularity#singularity-containers#slurm#workflow-engine

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