nf-explore

Learning how to use nextflow using paired-end RNA-seqeuncing data.

Installation:

To install this pipeline, please make sure you have nextflow installed.

conda create --name nextflow nextflow nf-core nf-test
conda activate nextflow

Now, you can clone this repository:

git clone https://github.com/kylacochrane/nf-explore.git
cd nf-explore

Running

To run this pipeline, pelase run:

nextflow run main.nf -profile singularity

Output files should be in results/

Parameters

Mandatory

Input: provided to nf-explore in the form of a samplesheet (passed as --input samplesheet.csv). This samplesheet is a CSV-formated file, which may be provided as a URL (ex: a file path or web address), and has the following format:

sample	fastq_1	fastq_2
SAMPLE1	/path/to/sample1_1.fastq.gz	/path/to/sample1_2.fastq.gz
SAMPLE2	/path/to/sample2_1.fastq.gz	/path/to/sample2_2.fastq.gz

The columns are defined as follows:

• sample: The unique sample identifier to associate with the reads
• fastq_1: A URI (ex: a file path or web address) to either single-end FASTQ-formatted reachs or one pair pf pair-end FASTQ-formatted reads.
• fastq_2: (Optional_ If fastq_1 is paired-end, then this field is a URI to other pair of reads.

Optional

• --genome: A URI to the reference genome to use during the pipeline analysis. Must be in FASTA-format.
• --outdir: The directory for pipeline output (DEFAULT: "results")

To run the tests:

nf-test test --profile singularity