rnatoy
A proof of concept RNA-Seq pipeline with Nextflow (by nextflow-io)
configs
Config files used to define parameters specific to compute environments at different Institutions (by nf-core)
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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.
rnatoy
Posts with mentions or reviews of rnatoy.
We have used some of these posts to build our list of alternatives
and similar projects.
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Nextflow RNA-seq pipeline
While running the https://github.com/nextflow-io/rnatoy/blob/master/main.nf pipeline, it throws me an error at line 64 : No such variable: genome. I have tried googling this error but I haven't found anything helpful so far.
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 rnatoy and configs you can also consider the following projects:
rnaseq-nf - A proof of concept of RNAseq pipeline
argo-events - Event-driven Automation Framework for Kubernetes
sarek - Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
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
eager - A fully reproducible and state-of-the-art ancient DNA analysis pipeline
mag - Assembly and binning of metagenomes