patterns
A curated collection of Nextflow implementation patterns (by nextflow-io)
configs
Config files used to define parameters specific to compute environments at different Institutions (by nf-core)
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| patterns | configs | |
|---|---|---|
| 1 | 1 | |
| 316 | 77 | |
| 1.3% | - | |
| 4.5 | 9.7 | |
| 5 months ago | 7 days ago | |
| Nextflow | Nextflow | |
| MIT License | MIT License |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
patterns
Posts with mentions or reviews of patterns.
We have used some of these posts to build our list of alternatives
and similar projects.
configs
Posts with mentions or reviews of configs.
We have used some of these posts to build our list of alternatives
and similar projects.
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Why does it feels impossible to set up github nextflow pipeline without a root?
To pick a random example config file (https://github.com/nf-core/configs/blob/master/conf/cambridge.config) - they have specified that singularity should be used, that the cluster's job scheduler is slurm and the maximum memory/time/cpus.
What are some alternatives?
When comparing patterns and configs you can also consider the following projects:
sarek - Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
argo-events - Event-driven Automation Framework for Kubernetes
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
eager - A fully reproducible and state-of-the-art ancient DNA analysis pipeline
rnaseq-nf - A proof of concept of RNAseq pipeline
rnatoy - A proof of concept RNA-Seq pipeline with Nextflow
mag - Assembly and binning of metagenomes