fix: Remove model filtering of logcount matrix

[fxwiegand]

This PR removes the filtering of the logcount matrices. This way they contain the same gene set across different defined models.

Summary by CodeRabbit

• New Features
  • Updated dataset configuration so that transcript links are now optional.
  • Modified data export to include all log count entries without filtering based on transcript presence.
• Bug Fixes
  • Disabled the filtering of columns containing only NA values in the samples data frame.

[coderabbitai]

Walkthrough

This pull request introduces updates across three files. In the configuration file, the link to transcripts entry under the logcount_matrix dataset now includes an optional: true property. The Python postprocessing script has been modified to remove a filtering step that previously excluded rows based on transcript values, resulting in the full logcount matrix being saved. In the R initialization script, minor formatting adjustments have been made, including changed indentation and commenting out code that removed columns containing only NA values.

Changes

File(s)	Change Summary
workflow/.../diffexp-template.yaml	Added the optional: true property to the link to transcripts entry in the logcount_matrix dataset links.
workflow/.../postprocess_logcount.py	Removed the filtering step that selected rows based on transcript values; now the original logcount_matrix is written directly to the output TSV file.
workflow/.../sleuth-init.R	Adjusted formatting with changes to the indentation of the drop_na function and commented out code that removed columns with only NA values.

Sequence Diagram(s)

sequenceDiagram
    participant Caller as User/Pipeline
    participant Script as Postprocess Logcount Script
    participant FS as File System
    Caller->>Script: Trigger postprocess
    Script->>FS: Read logcount_matrix TSV
    Script-->>Script: Load logcount_matrix DataFrame
    Note over Script: Filtering step removed
    Script->>FS: Write full logcount_matrix to output TSV
    FS-->>Script: Confirm write operation
    Script->>Caller: Signal completion

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Possibly related PRs

• feat: Add TPM matrix generation and integration into workflow #146: The changes in the main PR, which add an optional: true property to the link to transcripts entry in the diffexp-template.yaml, are related to the modifications in the retrieved PR that also involve the diffexp-template.yaml file, specifically adding a similar optional: true flag for the link to transcripts under the new tpm_matrix dataset.

Suggested reviewers

• johanneskoester

Poem

I hop with glee in lines of code so bright,
Optional paths now guide the links just right.
Filtering steps have taken a gentle leap away,
And tidy spacing makes the R code sway.
With every change, my whiskers twitch and play—
A rabbit’s cheer for a brighter coding day! 🐇

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📥 Commits

Reviewing files that changed from the base of the PR and between 60b6958 and 7886e0f.

📒 Files selected for processing (1)

• workflow/resources/datavzrd/diffexp-template.yaml (1 hunks)

🚧 Files skipped from review as they are similar to previous changes (1)

• workflow/resources/datavzrd/diffexp-template.yaml

⏰ Context from checks skipped due to timeout of 90000ms (2)

• GitHub Check: run-rna-workflow
• GitHub Check: run-three-prime-rna-workflow

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