agusinac/autoflow repository overview

⁠📋 Metadata File Specification

OmicFlow expects your sample metadata to follow a simple, but strict structure so that all datasets are compatible and validated up‑front.
Your metadata should be provided as a CSV (or TSV) file where each row = one sample and the first line should be a header. Additional columns are allowed and will be ignored during the metadata validation step.

⁠Minimum requirement

• SAMPLE_ID ➡ every row must have a unique, non‑empty sample identifier.
• No spaces are allowed in IDs — use underscores _ or dashes - instead.

Example:

⁠Column types and naming rules

⁠🔹 Required column

⁠🔹 Optional standard columns

⁠🔹 Pattern‑based columns

You can define extra variables using special prefixes:

• CONTRAST_... → grouping/category labels used in differential comparisons
  Example: CONTRAST_Treatment with values Drug / Placebo
• VARIABLE_... → numeric or string variables for statistical analysis
  Example: VARIABLE_Age with values 42, 51, etc.

The pattern-based columns are only used during the autoFlow function. At the moment only columns with prefix CONTRAST_ are supported.

NOTE: Symbolic links do not work with mounting, please only copy the original file!

Example: Outputs a report.html file in current work directory

docker run -it --rm -v \
    "$(pwd)":/data \             # Mount the data in a temporary directory
    -w /data \                   # set working directory
    -u $(id -u):$(id -g) \       # non-root user
    agusinac/autoflow:1.4.0 \
    autoflow \                   # autoflow R script
    -b /data/biom_with_taxonomy_hdf5.biom \
    -m /data/metadata.tsv

For additional options please run autoflow -h

⁠Support

If you are having issues, please create an issue⁠