Top 7 Nextflow nextflow Projects
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.
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
Run Linux Software Faster and Safer than Linux with Unikernels.
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencingProject mention: Workflow Question | reddit.com/r/bioinformatics | 2021-07-09
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
A fully reproducible and state-of-the-art ancient DNA analysis pipelineProject 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 ;)
A proof of concept of RNAseq pipelineProject 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
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.
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Generate consensus FASTA files pipeline
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Why does it feels impossible to set up github nextflow pipeline without a root?
1 project | reddit.com/r/bioinformatics | 7 Jul 2021
Nextflow RNA-seq pipeline
1 project | reddit.com/r/bioinformatics | 27 Mar 2021
aws batch keeps the "Desired vCPUs" high long after they should be reduced
1 project | reddit.com/r/aws | 15 Mar 2021
Snakemake vs. nf vs. CWL
1 project | reddit.com/r/bioinformatics | 1 Mar 2021
Nextflow question config
1 project | reddit.com/r/bioinformatics | 6 Feb 2021
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