Figure : CWL description of MAW workflow and its sub-workflows for the execution of a single .mzML file. The environment setup with all the dependencies is provided via Docker-format software container images, one defined for each sub-workflow of MAW (dereplication -MAW-R, metfrag -MAW-MetFrag, and cheminformatics -MAW-Py). The first section in the figure showcases all the workflow inputs, including the R and Python scripts, the input .mzML file, the paths to spectral databases (hmdb_file, gnps_file, mbank_file), the information on collision energy used to fragment the molecules (collision_info), the relative mass deviation in parts per million (ppm), and finally the compound database name and its path (db_name, db_path, which is the COCONUT database). The dereplication step (MAW-R) takes all inputs except the python script. Once dereplication is executed, Metfrag takes the parameters generated from dereplication step such as (IonizedPrecursorMass, PeakList, SampleName, and PrecursorIonMode). Once metfrag step is also executed, cheminformatics (MAW-Py) step takes outputs from dereplication (gnps_dir, ms1data, hmdb_dir, msp_file, mbank_dir) and metfrag steps (metfrag_candidate_list), and generates final outputs, the candidate files (candidates lists for each molecule), and result (final top 1st candidate list for all molecules). The inputs are provided via a YAML file. This whole workflow can be scattered over multiple .mzML input files for parallelisation.