capellini.stages.dada2

DADA2 stage: run DADA2_Pipe.R and move the generated FASTA.

Functions

run_dada2(cfg)

Run the DADA2_Pipe.R script and move the output FASTA to the input folder.

capellini.stages.dada2.run_dada2(cfg: CapelliniConfig) → Path

Run the DADA2_Pipe.R script and move the output FASTA to the input folder.

The R script is called with six arguments matching the notebook:

Rscript DADA2_Pipe.R <bacterial_raw_fasta_folder> <dada2_folder>

<silva_ref_path> <silva_taxmap_path> <direction> <TRUE|FALSE>

After the run the produced ASV_sequences_{F|R|P}.fasta is moved to cfg.input_fasta_folder / cfg.bacteria_fasta_name.

Parameters:

cfg – Populated CapelliniConfig instance.

Returns:

Path to the moved bacteria FASTA file.

Raises:

• FileNotFoundError – If the FASTA is not found after the R run.

• subprocess.CalledProcessError – If Rscript exits non-zero.