Setting up a portable RNA-Seq pipeline for CBIO

Pertinent points for setup of NGI-RNAseq pipeline on UCT hex
*Pipeline source code is at https://github.com/SciLifeLab/NGI-RNAseq
*Additional overview on NGI-RNAseq pipeline at https://scilifelab.github.io/courses/rnaseq/1711/slides/pipeline.pdf
*Software requirements will be met using Singularity - the image has been downloaded and stored here /scratch/DB/bio/singularity-containers/ngi-rnaseq.img using the command: singularity pull --name ngi-rnaseq.img docker://scilifelab/ngi-rnaseq
* First test: nextflow run SciLifeLab/NGI-RNAseq --help
* Reference genomes and annotation files should be placed in /scratch/DB/bio/rna-seq (will pull iGenomes GRCh37 to here)
* For reproducibility please specify the pipeline version used when running the pipeline using the -r flag (e.g. –r 1.3.1)
* If using Illumina's iGenomes for reference genomes as recommended the following line should be included in the nextflow.config file includeConfig '/path/to/NGI-RNAseq/conf/igenomes.config' The igenomes.config can be used as is if we download an iGenomes reference genome, but need to specify path in nextflow.config by creating a $params.igenomes_base parameter
* The nextflow.config file also needs to be configured to our setup on hex. The following was included in the nextflow.config file to configure to hex:
1. docker.enabled = false
singularity.enabled = true
singularity.cacheDir = "/scratch/DB/bio/singularity-containers"
2. profiles{
standard {
process.executor = 'local'
}

hex {
//The next 3 lines includeConfig from the NGI-RNAseq nextflow.config not sure if they need to be changed
includeConfig 'conf/base.config'
//Think the singularity.config line can be excluded see https://github.com/SciLifeLab/NGI-RNAseq/blob/master/conf/singularity.config
includeConfig 'conf/singularity.config'
includeConfig 'conf/igenomes.config'
//The remaining lines are from Gerrit's nextflow.config for 16S pipeline
process.executor = 'pbs'
process.queue = 'UCTlong'
process.clusterOptions = '-M katie.viljoen@uct.ac.za -m abe -l nodes=1:ppn=1:series600'
}
}
3. Specify where iGenomes reference to be found (and other parameters can be defined here):
params {

igenomes_base = '/scratch/DB/bio/rna-seq/'
clusterOptions = false
outDir = "/researchdata/fhgfs/katie/NGI-RNAseq-test/nextflow-output"

}

* The basic run will look something like this:
nextflow run SciLifeLab/NGI-RNAseq -with-singularity /scratch/DB/bio/singularity-containers/ngi-rnaseq.img --reads '*_R{1,2}.fastq.gz' --genome GRCh37 -profile hex
* Human RNAseq test data to be used: http://h3data.cbio.uct.ac.za/assessments/RNASeq/practice/ (downloaded to /researchdata/fhgfs/katie/NGI-RNAseq-test)
* First test run:
> * qsub -I -q UCTlong -d `pwd`
> * nextflow run SciLifeLab/NGI-RNAseq -with-singularity /scratch/DB/bio/singularity-containers/ngi-rnaseq.img --reads '/researchdata/fhgfs/katie/NGI-RNAseq-test/*_R{1,2}.fastq.gz' --genome GRCh37 --outdir /researchdata/fhgfs/katie/NGI-RNAseq-test/nextflow-output -profile hex