Nextflow nextflow

Open-source Nextflow projects categorized as nextflow | Edit details

Top 7 Nextflow nextflow Projects

  • GitHub repo rnaseq

    RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

    Project mention: Tkinter for python 3.10 broken on MacOS? | reddit.com/r/Python | 2021-10-07

    Not really sure why it's a problem for you, I'm working on rnaseq and they use a very big input dataset, also outputs huge datasets too. It uses docker so you can deploy fast on VMs.

  • GitHub repo patterns

    A curated collections of Nextflow implementation patterns -- http://nextflow-io.github.io/patterns/index.html (by nextflow-io)

    Project mention: Nextflow question config | reddit.com/r/bioinformatics | 2021-02-06
  • Nanos

    Run Linux Software Faster and Safer than Linux with Unikernels.

  • GitHub repo sarek

    Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

    Project mention: Workflow Question | reddit.com/r/bioinformatics | 2021-07-09
  • GitHub repo mag

    Assembly and binning of metagenomes (by nf-core)

    Project mention: Is it possible to assemble a complete bacterial genome using short reads? | reddit.com/r/bioinformatics | 2021-08-09
  • GitHub repo eager

    A fully reproducible and state-of-the-art ancient DNA analysis pipeline

    Project mention: Generate consensus FASTA files pipeline | reddit.com/r/ngs | 2021-07-14

    So after a lot of reading and talking with some people i was able to do it with the eager pipeline (https://github.com/nf-core/eager) migth be a bit dificult to set up, but it is really useful. I leave this here for you and other people that may see this ;)

  • GitHub repo rnaseq-nf

    A proof of concept of RNAseq pipeline

    Project mention: Snakemake vs. nf vs. CWL | reddit.com/r/bioinformatics | 2021-03-01

    For example look at: https://github.com/nextflow-io/rnaseq-nf/blob/master/nextflow.config#L39

  • GitHub repo configs

    Config files used to define parameters specific to compute environments at different Institutions (by nf-core)

    Project mention: Why does it feels impossible to set up github nextflow pipeline without a root? | reddit.com/r/bioinformatics | 2021-07-07

    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.

  • Scout APM

    Scout APM: A developer's best friend. Try free for 14-days. Scout APM uses tracing logic that ties bottlenecks to source code so you know the exact line of code causing performance issues and can get back to building a great product faster.

NOTE: The open source projects on this list are ordered by number of github stars. The number of mentions indicates repo mentiontions in the last 12 Months or since we started tracking (Dec 2020). The latest post mention was on 2021-10-07.

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Index

What are some of the best open-source nextflow projects in Nextflow? This list will help you:

Project Stars
1 rnaseq 396
2 patterns 201
3 sarek 125
4 mag 68
5 eager 61
6 rnaseq-nf 38
7 configs 37
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