Pairwise Genome Comparison Statistics

Mandatory parameters

• --input: path to a sample sheet in tab-separated format with one header line id file, and one row per genome (ID and path to FASTA file).

Optional parameters

• --skel: path or URL to a "skeletton" Rmarkdown file.

Run

See the makeGBreaksInputFile.sh script in oist/LuscombeU_ScramblingInTheTreeOfLife for an example on how to construct an input file. Then, run the pipeline. If needed, do not forget to give a path to a work directory writable by the compute node (at OIST, it is on the /flash file system) using the -w option.

nextflow run oist/plessy_nf_GenomicBreaks -r main -profile oist --input input.tsv

Test

To test the pipeline, just run it with the input file from GitHub. This will download a small alignment file between a SARS-CoV-2 genome and a SARS-CoV-2 contig assembly.

nextflow run oist/plessy_nf_GenomicBreaks -r main -profile oist --input https://github.com/oist/plessy_nf_GenomicBreaks/raw/main/input.tsv

Tip

Cache the singularity image to avoid multiple downloads, using the singularity.cacheDir option in ~/.nextflow/config.