usage.md

RNA-seq_VAX Usage

This pipeline is still in alpha stage. please use at your own cause

General Nextflow info

Nextflow handles job submissions on SLURM or other environments, and supervises running the jobs. Thus the Nextflow process must run until the pipeline is finished. We recommend that you put the process running in the background through screen / tmux inside a .sh or similar tool. Alternatively you can run nextflow within a cluster job submitted your job scheduler.

It is recommended to limit the Nextflow Java virtual machines memory. We recommend adding the following line to your environment (typically in ~/.bashrc or ~./bash_profile):

NXF_OPTS='-Xms1g -Xmx6g'

Running the pipeline

The typical command for running the pipeline is as follows:

    nextflow run RNAseq_VAX  -with-singularity rnaseq_vax.sif --project 'your_uppmax_project' --genome /sw/data/uppnex/reference/Homo_sapiens/hg19/program_files/GATK/concat.fasta

This will launch the pipeline with the singularity configuration profile. See below for more information about profiles.

Note that the pipeline will create the following files in your working directory:

work            # Directory containing the nextflow working files
results         # Finished results (configurable, see below)
.nextflow_log   # Log file from Nextflow
# Other nextflow hidden files, eg. history of pipeline runs and old logs.

Updating the pipeline

When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline:

nextflow pull rna-seq_VAX