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Pipeline DAG

Source: vignettes/pipeline-dag.qmd

Online documentation

This vignette shows pre-computed results from the targets pipeline.

Pipeline Overview

The CoMMpass analysis pipeline is organized into isolated layers. Each layer corresponds to a functional area of the analysis, with explicit allowed dependencies between layers.

Layer Description
data-acquisition Download RNA-seq and clinical data from GDC
data-cleaning Standardize and integrate datasets
cytogenetics Extract FISH markers and classify risk
quality-control Sample QC, filtering, normalization
differential-expression DESeq2, edgeR, limma-voom analysis
survival Kaplan-Meier, Cox PH regression
pathway GSEA, ORA, gene annotation
eda Exploratory summaries
storage DuckDB/parquet querying
api Plumber API for programmatic access
documentation Vignette pre-computed outputs
infrastructure Nix sync, pkgctx, DAG validation

DAG Validation

Validation checks on the targets pipeline DAG: no orphaned targets, no circular dependencies, and all vignette targets are reachable from raw data inputs. A passing validation confirms the pipeline is structurally sound.

DAG layer validation: 183 targets across 13 layers. All layers pass structural checks.
Layer Targets Status
documentation 96 Pass
api 23 Pass
other 18 Pass
eda 9 Pass
survival 8 Pass
infrastructure 7 Pass
data-cleaning 5 Pass
differential-expression 5 Pass
cytogenetics 4 Pass
pathway 3 Pass
data-acquisition 2 Pass
quality-control 2 Pass
storage 1 Pass

Target Network

Interactive DAG showing the targets pipeline network with layer-based coloring. Nodes are colored by functional layer. Hover for target details, use the dropdown to search by name.

Interactive widget available in local builds only. Interactive DAG available in local builds only.

Run targets::tar_visnetwork(targets_only = TRUE) locally.

Pipeline by Layer

To explore the full interactive DAG locally, run:

targets::tar_visnetwork(targets_only = TRUE, label = "time")

Recent Changes

Recent project commits with lines added, files changed, and change categories.

Last 20 project commits with change statistics. Date = commit date; Type = conventional-commit prefix (feat/fix/docs/ci/refactor/test/chore). Files = number of files modified; +Lines/-Lines = lines added/removed. Source: git log –numstat. See changes-by-type table for aggregate breakdown.
date type summary n_files lines_added lines_removed file_categories
2026-03-14 Bug Fix fix(pipeline): Fix 11 NULL targets — DE condition, ID matching, consensus type 41 146 47 Other, R Source
2026-03-14 Bug Fix fix(cachix): Remove –watch-mode auto flag (already default) 1 1 1 Other
2026-03-14 Bug Fix fix(pipeline): Fix 3 NULL-target bugs, auto-generate package.nix (#93) 87 235 80 Config, Docs, Other, R Source
2026-03-14 Bug Fix fix(nix): Fix cachix signing key, rebuild Bioconductor-dependent targets 2 0 0 Other
2026-03-14 New Feature feat(captions): Add dynamic captions to 34 table/plot targets 22 579 89 Other, R Source
2026-03-14 Bug Fix fix(vignettes): Enforce zero-computation rule — 22 violations → 0 32 360 764 Other, R Source, Vignettes
2026-03-13 Bug Fix fix(vignettes): Convert kable RDS to data.frames, fix telemetry eval guards 18 8 2 Other, Vignettes
2026-03-13 Bug Fix fix(ci): Save data frames (not DT widgets) to RDS for Nix portability 3 0 0 Other
2026-03-13 Bug Fix fix(vignettes): Use Quarto #| eval syntax for pkgdown-banner chunks 11 44 11 Vignettes
2026-03-13 Refactoring refactor(targets): Move Bioconductor packages to per-target declarations 11 35 17 Other, R Source, Vignettes
2026-03-13 New Feature feat(vignettes): Add code provenance, kable→DT conversion, caption compliance 35 1004 437 CI/CD, Other, R Source, Vignettes
2026-03-13 Bug Fix fix(vignettes): Skip NULL RDS in safe_tar_read, return invisible(NULL) 11 22 22 Vignettes
2026-03-13 Bug Fix fix(glossary): Prevent double DT::datatable() wrapping in glossary-table chunk 1 3 1 Vignettes
2026-03-13 CI/CD ci: Show quarto errors with quiet=FALSE, render individual vignettes in diagnostic 1 20 6 CI/CD
2026-03-13 CI/CD ci: Add verbose quarto error diagnostics on build failure 1 14 1 CI/CD
2026-03-13 Bug Fix fix(vignettes): Strip Nix paths from DT widgets, auto-wrap data frames 25 66 28 CI/CD, Other, Vignettes
2026-03-13 CI/CD ci: Add diagnostic quarto render step to debug build failure 1 17 0 CI/CD
2026-03-13 Bug Fix fix(vignettes): Revert safe_tar_read placeholder, guard gene-report 11 12 56 Vignettes
2026-03-13 Maintenance chore: Export vig_count_distribution_plot as ggplot RDS (513KB) 1 0 0 Other
2026-03-13 Bug Fix fix(vignettes): Enable code eval in CI with RDS fallback 80 113 74 CI/CD, Other, R Source, Vignettes

Reproducibility

Session Info (click to expand)
Show code
sessionInfo()
#> R version 4.5.3 (2026-03-11)
#> Platform: x86_64-pc-linux-gnu
#> Running under: Ubuntu 24.04.3 LTS
#> 
#> Matrix products: default
#> BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3 
#> LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so;  LAPACK version 3.12.0
#> 
#> locale:
#>  [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8       
#>  [4] LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8    LC_MESSAGES=C.UTF-8   
#>  [7] LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C          
#> [10] LC_TELEPHONE=C         LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   
#> 
#> time zone: UTC
#> tzcode source: system (glibc)
#> 
#> attached base packages:
#> [1] stats     graphics  grDevices utils     datasets  methods   base     
#> 
#> loaded via a namespace (and not attached):
#>  [1] vctrs_0.7.2         cli_3.6.5           knitr_1.51         
#>  [4] rlang_1.1.7         xfun_0.57           otel_0.2.0         
#>  [7] processx_3.8.6      targets_1.12.0      jsonlite_2.0.0     
#> [10] data.table_1.18.2.1 glue_1.8.0          prettyunits_1.2.0  
#> [13] backports_1.5.0     htmltools_0.5.9     ps_1.9.1           
#> [16] rmarkdown_2.30      tibble_3.3.1        evaluate_1.0.5     
#> [19] base64url_1.4       fastmap_1.2.0       yaml_2.3.12        
#> [22] lifecycle_1.0.5     compiler_4.5.3      codetools_0.2-20   
#> [25] igraph_2.2.2        pkgconfig_2.0.3     digest_0.6.39      
#> [28] R6_2.6.1            tidyselect_1.2.1    pillar_1.11.1      
#> [31] callr_3.7.6         magrittr_2.0.4      withr_3.0.2        
#> [34] tools_4.5.3         secretbase_1.2.0