Facilitate iteration in differential subworkflow

[pinin4fjords]

Objective

To facilitate iterative plans proposed by community members for the differentialabundance pipeline.

Key Changes

1. Iterative Processing

   • Introduce ch_inputs channel for iterative content
   • Contents: meta, abundance matrix, and analysis method, plus thresholds (since these might be dependent on method etc)

2. Static Inputs

   • Contrasts and sample sheet treated as once-per-pipeline inputs
   • Combined with ch_inputs using Nextflow's combine operator

3. Module Parameterization

   • DESeq2 and limma modules receive matrix-level meta
   • Enables custom parameters via closures in pipeline modules.conf

Implementation

• Iterate through input matrices and parameter sets for all specified contrasts
• Use combine operation to merge static and iterative inputs

This is quite like the differential subworkflow proposal in https://github.com/nf-core/differentialabundance/pull/288/files, except:

• Single multiMap required
• No duplication of filtering subworkflow import
• Reduced need to muck about with meta combinations in the subworkflow
• No assumptions about meta elements (method is part of the main channel content)

PR checklist

Closes #XXX

• This comment contains a description of changes (with reason).
• If you've fixed a bug or added code that should be tested, add tests!
• If you've added a new tool - have you followed the module conventions in the contribution docs
• If necessary, include test data in your PR.
• Remove all TODO statements.
• Emit the versions.yml file.
• Follow the naming conventions.
• Follow the parameters requirements.
• Follow the input/output options guidelines.
• Add a resource label
• Use BioConda and BioContainers if possible to fulfil software requirements.
• Ensure that the test works with either Docker / Singularity. Conda CI tests can be quite flaky:
  • For modules:
    • nf-core modules test <MODULE> --profile docker
    • nf-core modules test <MODULE> --profile singularity
    • nf-core modules test <MODULE> --profile conda
  • For subworkflows:
    • nf-core subworkflows test <SUBWORKFLOW> --profile docker
    • nf-core subworkflows test <SUBWORKFLOW> --profile singularity
    • nf-core subworkflows test <SUBWORKFLOW> --profile conda

[pinin4fjords]

Just trying to track down the cryptic timezone issues in the CI...