amalgkit sanity

Overview

amalgkit sanity scans the working directory to verify the presence of all outputs for both quant and amalgkit getfastq for every sample listed in metadata.tsv. It also checks for the requisite index files for quantification. If any discrepancies are detected, such as a missing expression file for a sample from amalgkit quant, amalgkit sanity promptly notifies the user. This function proves particularly beneficial when handling vast numbers of samples, as manual verification of all outputs becomes cumbersome.

Usage

To check for the presence of FASTA index files, outputs from amalgkit quant, and outputs from amalgkit getfastq, use the following command. If certain checks are not required, simply omit the corresponding arguments.

amalgkit sanity --metadata /PATH/TO/metadata.tsv --out_dir /WORKING/DIRECTORY/ --index --quant --getfastq

For a comprehensive check, you can use the --all option:

amalgkit sanity --metadata /PATH/TO/metadata.tsv --out_dir /WORKING/DIRECTORY/ --all

STDOUT will display information about any missing files and suggest appropriate commands to rerun the missing samples.