agusinac/autoflow
agusinac
R image for the running of the autoFlow.R script: https://github.com/agusinac/OmicFlow
下载次数: 0状态：社区镜像维护者：agusinac仓库类型：镜像最近更新：4 个月前
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📋 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:
| SAMPLE_ID | FEATURE_ID | SAMPLEPAIR_ID | CONTRAST_Treatment | VARIABLE_Age |
|---|---|---|---|---|
| S1 | OTU0001 | P1 | Drug | 42 |
| S2 | OTU0002 | P1 | Placebo | 36 |
| S3 | OTU0003 | P2 | Drug | 51 |
Column types and naming rules
🔹 Required column
| Column | Type | Rules |
|---|---|---|
SAMPLE_ID | string | Unique, no spaces, one per sample row |
🔹 Optional standard columns
| Column | Type | Rules |
|---|---|---|
FEATURE_ID | string | Optional — no spaces. Naming of the feature identifiers to include or exclude certain features |
SAMPLEPAIR_ID | string | Optional — no spaces. Use when samples are paired and belong to an individual source/subject |
🔹 Pattern‑based columns
You can define extra variables using special prefixes:
CONTRAST_...→ grouping/category labels used in differential comparisons
Example:CONTRAST_Treatmentwith valuesDrug/PlaceboVARIABLE_...→ numeric or string variables for statistical analysis
Example:VARIABLE_Agewith values42,51, 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
bashdocker 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 https://github.com/agusinac/OmicFlow/issues
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