new module: metaproviz/internalstandard

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Further Information

Proposed module: metaproviz/internalstandard

This is the first of multiple nf-core modules for a metabolomics workflows. All modules will cover metabolomics processing, QC of data and features, which builds upon existing raw data workflow of metaboigniter and would use its output.

This module internalstandard computes each internal standard's coefficient of variation (CV) across all real samples. Pool and QC samples are excluded, since their already-pooled nature would understate true injection-to-injection variability. A high CV indicates instrument drift or injection issues rather than biological variation.

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Software requirements (conda)

---
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
channels:
  - conda-forge
  - bioconda
dependencies:
  - r-base=4.6.1
  - bioconductor-summarizedexperiment=1.42.0
  - bioconductor-s4vectors=0.50.1
  - r-dplyr=1.1.4
  - r-tidyr=1.3.1
  - r-tibble=3.2.1
  - r-magrittr=2.0.3
  - r-ggplot2=3.5.1
  - r-base64enc=0.1_3
  - r-remotes=2.5.0
  # MetaProViz itself is not on bioconda — installed separately via
  # BiocManager::install() into a custom image; see note above.

Start with the proposed metaproviz/internalstandard module and its listed conda dependency block. Read the existing nf-core module conventions and determine how inputs, outputs, exclusions for pool and QC samples, and testing are represented. Done means the module computes internal-standard CVs across real samples and has reproducible environment and validation coverage.