Genome to Proteome Alignment

Mandatory parameters

• --target: path to one proteome file in FASTA format.

  — or —

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

• --query: path to one genome file in FASTA format.

Options

• --lastdb_args defaults to -q -c -R01 , like in the LAST cookbook.

• --train_args defaults to --codon -X1 .

• --lastal_args defaults to -D1e9 -m100 -K1 .

• --format defaults to gff . Can be converted to a standard GFF with a custom script and uploaded to ZENBU for viewing.

Test

test remote

nextflow run aleksandrabliznina/LuscombeU_GenomeToProteome -r main -profile oist --input testInput.tsv --query https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta
nextflow run aleksandrabliznina/LuscombeU_GenomeToProteome -r main -profile oist --target https://raw.githubusercontent.com/aleksandrabliznina/LuscombeU_GenomeToProteome/main/sarscov2.protein.fasta --query https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta

test locally

nextflow run ./main.nf -profile oist --input testInput.tsv --query https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta
nextflow run ./main.nf -profile oist --target https://raw.githubusercontent.com/aleksandrabliznina/LuscombeU_GenomeToProteome/main/sarscov2.protein.fasta --query https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/genomics/sarscov2/genome/genome.fasta

Advanced use

Override computation limits

Computation resources allocated to the processe are set with standard nf-core labels in the nextflow.config file of the pipeline. To override their value, create a configuration file in your local directory and add it to the run's configuration with the -c option.

For instance, with file called overrideLabels.nf containing the following:

process {
  withLabel:process_high {
    time = 3.d
  }
}

The command nextflow -c overrideLabels.nf run … would set the execution time limit for the training and alignment (whose module declare the process_high label) to 3 days instead of the 1 hour default.

Semantic versioning

I will apply semantic versioning to this pipeline:

• Major increment when the interface changes in a way that is backwards-incompatible, in the sense that a run with the same command and the same data would produce a different result (except for non-deterministic computations).

• Minor increment for any other change of the interface, such as additions of new functionalities.

• Patch increment for changes that do not modify the interface (bug fixes, minor software and module updates, documentation changes, etc.)