This pipeline analyses data from full-length single-cell RNA sequencing (scRNA-seq) methods.
The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.
i. Install nextflow
ii. Install either Docker
or Singularity
for full pipeline reproducibility (see docs). Note that ramdaq does not support conda.
iii. Download the pipeline automatically and test it on a minimal dataset with a single command
1. Example of test using Docker
nextflow run rikenbit/ramdaq -profile test,docker
2. Example of test using Singularity
nextflow run rikenbit/ramdaq -profile test,singularity
iv. Start running your own analysis!
iv-i. You can run ramdaq without donwloading reference annotation data.
nextflow run rikenbit/ramdaq -profile <docker/singularity> --reads '*_R{1,2}.fastq.gz' --genome GRCh38_v37
iv-i. You can also run ramdaq by specifying local paths to reference annotation (See 'Using provided reference genome and annotations').
nextflow run rikenbit/ramdaq -profile <docker/singularity> --reads '*_R{1,2}.fastq.gz' --genome GRCh38_v37 --local_annot_dir <The directory path where the reference genome and annotations are placed>
See usage docs for all of the available options when running the pipeline.
To download or update ramdaq, run nextflow pull
:
nextflow pull rikenbit/ramdaq
To check the available versions, run nextflow info
:
nextflow info rikenbit/ramdaq
The above command will return the message like this (* master (default)
indicates that the latest version will be used when you execute nextflow run rikenbit/ramdaq ...
):
$ nextflow info rikenbit/ramdaq
project name: rikenbit/ramdaq
repository : https://github.com/rikenbit/ramdaq
local path : /Users/haruka/.nextflow/assets/rikenbit/ramdaq
main script : main.nf
description : This pipeline analyses data from full-length single-cell RNA sequencing (scRNA-seq) methods.
author : Mika Yoshimura and Haruka Ozaki
revisions :
* master (default)
dev
1.0 [t]
1.1 [t]
To use versions other than the latest version, use -r
to set the version name as follows:
nextflow run rikenbit/ramdaq -r 1.1 ...
The ramdaq pipeline comes with documentation about the pipeline, found in the docs/
directory:
ramdaq is written and maintained by Mika Yoshimura and Haruka Ozaki in the collaboration of Laboratory for Bioinformatics Research, RIKEN Center for Biosystems Dynamics Research and Bioinformatics Laboratory, Faculty of Medicine, University of Tsukuba.
ramdaq was originally developed based on the nf-core template.