A DSL for data-driven computational pipelines

aws bioinformatics cloud dataflow docker groovy hello hpc nextflow pipeline pipeline-framework reproducible-research reproducible-science sge singularity singularity-containers slurm workflow-engine
3 Open Issues Need Help Last updated: Sep 14, 2025

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Add hyperlinks to HTML DAG about 2 months ago
stale good first issue

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

AI Summary: Implement support for shallow cloning of git submodules within Nextflow, allowing users to specify clone depth via CLI arguments or `.gitmodules` configuration, addressing performance issues when dealing with repositories containing large submodules with extensive commit history.

Complexity: 4/5
software/git good first issue

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

AI Summary: Enhance the Nextflow execution report to include a cumulative real-time duration for each process, visualized as a bar plot in a new tab within the existing Job Duration section. This will help users identify processes with high cumulative runtimes, even if individual execution times are short, facilitating performance optimization.

Complexity: 4/5
good first issue

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