ZARP: Supplementary materials

This record supplements the F1000Research article on the ZARP workflow and its ZARP-cli command-line interface.

The following data are included:

• zarp_use_cases.zip: Includes instructions (zarp_use_cases.md) and input data required to reproduce the use cases described in the manuscript.
• mouse_sarcopenia_example_outputs.zip: Contains the cross-sample outputs (gene/transcript expression tables, PCA, MultiQC report and Snakemake report) produced by a ZARP run for the described 20-sample mouse sarcopenia RNA-seq experiment (not including indexes), as well as the sample-specific outputs for the smallest of the 20 samples.
• zarp_cli_example_outputs.zip: Contains a representative fraction of the outputs produced by the described ZARP-cli runs; in particular, it contains the artifacts generated by the SRA download workflow for a single C. elegans sample (SRR21711080), the outputs produced by the HTSinfer workflow for all 25 samples (20 from the mouse sarcopenia dataset and 5 from the metadata inference demonstration run), the genome resources created by genomepy for the C. elegans genome WBcel235, and the C. elegans-specific ZARP workflow results, including indexes.

We would further like readers to note the following:

• With respect to the latter two archives, data were selected in an effort to keep the record at an acceptable size, while still providing a representative and largely complete overview of ZARP and ZARP-cli outputs for reference and validation.
• In all cases where files contained absolute file paths, we have manually replaced the real path prefixes with a dummy value (PATH/TO/MY/ANALYSIS), in order not to expose potentially sensitive details about the file system the analyses were run on.
• We have deliberately not included ZARP, ZARP-cli and machine logs, as we feel that these may be too system-specific and potentially sensitive; we do, however, retain all logs in our archive, and will be willing to share them in response to reasonable requests.