CompareTE

A pipeline to compare TE content across genomes using various platforms.

Requirements

Requires Nextflow >=26.04.

Input

Input should be a csv file (ending in .csv).

It should contain either:

name,refseqID
name,/full/path/to/genome.fa 
name,/full/path/to/genome.fa,/full/path/to/annotation.gff

!! Do not use relative paths !!

The genome must end with:

'.fa', '.fasta', '.fna', '.fa.gz', '.fasta.gz', '.fna.gz'

The annotation must end with:

'.gff', '.gff3', '.gff.gz', '.gff3.gz'

See examples in conf/test (various example in config files)

Running the pipeline

To run the pipeline you need to make a csv input file as described above with either Refseq IDs (these always begin GCF_…), or with genomes, or genomes and annotation files.

To run with all the different TE programs on a input csv file called input.csv:

nextflow run main.nf --orthofinder --hite --earlgrey --input input.csv

Though, the above would require you to manually download all the prerequisites and programs, so the easier way is to set a container engine to pull all the programs you need:

nextflow run main.nf --orthofinder --hite --earlgrey --input input.csv -profile docker/singularity/apptainer

HPC cluster profiles

Bundled institutional profiles configure the scheduler, container engine, and resource limits for a specific cluster. They already enable the right container engine, so you do not need to add -profile singularity or an external -c config.

Combine an HPC profile with a test or input profile, e.g. on UCL Myriad:

nextflow run main.nf -profile ucl_myriad,test_bacteria -resume --hite

On Cambridge CSD3, export your SLURM project/account first (defaults to the icelake partition):

export NXF_CAMBRIDGE_PROJECT=MYPROJECT-SL2-CPU
nextflow run main.nf -profile cambridge,test_bacteria -resume --hite

Useful additional flags:

-resume : This allows the pipeline to resume from the last failed process (using the nextflow cache-ing mechanism) -bg : This allows nextflow to run in the background, so you can continue to use your terminal.

Current test commands:

nextflow run main.nf -profile docker,test_bacteria -resume

To run with HITE:

nextflow run main.nf -profile docker,test_bacteria -resume --hite

To run with EARL GREY:

nextflow run main.nf -profile docker,test_bacteria -resume --earlgrey

To run orthofinder on your input species:

nextflow run main.nf -profile docker,test_bacteria -resume --orthofinder

Test a docker container:

docker run -it --volume $PWD:$PWD <container> bash