rnaseq-nf
A proof of concept of RNAseq pipeline (by nextflow-io)
configs
Config files used to define parameters specific to compute environments at different Institutions (by nf-core)
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rnaseq-nf | configs | |
---|---|---|
1 | 1 | |
62 | 77 | |
- | - | |
5.8 | 9.7 | |
18 days ago | 5 days ago | |
Nextflow | Nextflow | |
Mozilla Public License 2.0 | 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.
rnaseq-nf
Posts with mentions or reviews of rnaseq-nf.
We have used some of these posts to build our list of alternatives
and similar projects.
-
Snakemake vs. nf vs. CWL
For example look at: https://github.com/nextflow-io/rnaseq-nf/blob/master/nextflow.config#L39
configs
Posts with mentions or reviews of configs.
We have used some of these posts to build our list of alternatives
and similar projects.
-
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 rnaseq-nf 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
rnatoy - A proof of concept RNA-Seq pipeline with Nextflow
rnaseq - RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
patterns - A curated collection of Nextflow implementation patterns
rare-disease-wf - (WIP) best-practices workflow for rare disease
eager - A fully reproducible and state-of-the-art ancient DNA analysis pipeline
mag - Assembly and binning of metagenomes