Build branch save-params with version save-params (dbca5cb)

Build pipeline: viash-hub.htrnaseq.save-params-jsfjj

Source commit: dbca5cbb3a

Source message: Apply suggestions from code review

target/executable/report/create_report/.config.vsh.yaml

@@ -164,6 +164,12 @@ engines:
     - "procps"
     - "pandoc"
     interactive: false
+  - type: "r"
+    script:
+    - "install.packages(\"BiocManager\")"
+    - "BiocManager::install(version = \"3.21\", type = \"source\", checkBuilt = TRUE)"
+    bioc_force_install: false
+    warnings_as_errors: true
   - type: "r"
     cran:
     - "ggplot2"
@@ -205,18 +211,35 @@ build_info:
   engine: "docker|native"
   output: "target/executable/report/create_report"
   executable: "target/executable/report/create_report/create_report"
-  viash_version: "0.9.2"
-  git_commit: "cc910b428428dd32f183df0c2009fc36e75394e0"
+  viash_version: "0.9.4"
+  git_commit: "dbca5cbb3a338287f516c79705fc607bcf0905f7"
   git_remote: "https://github.com/viash-hub/htrnaseq"
+  git_tag: "v0.7.2-21-gdbca5cb"
 package_config:
   name: "htrnaseq"
   version: "save-params"
-  description: "High-throughput pipeline [WIP]\n"
+  summary: "A workflow for high-throughput RNA-seq data analyses.\n"
+  description: "This workflow is designed to process high-throughput RNA-seq data,\
+    \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
+    \ input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow\
+    \ is built in a modular fashion, where most of the base functionality\nis provided\
+    \ by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\n\
+    supplemented by custom base components and workflow components in this package.\n\
+    \nThe full workflow is split in two major subworkflows that can be run independently:\n\
+    \n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per\
+    \ well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate\
+    \ QC reports.\n\nEach of those can be started individually, or the full workflow\
+    \ can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq)\
+    \ \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner)\
+    \ where a\nnumber of choices (input/output structure and location) have been made.\n\
+    \nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other\
+    \ formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex)\
+    \ first.\n"
   info:
     test_resources:
     - path: "gs://viash-hub-test-data/htrnaseq/v1/"
       dest: "resources_test"
-  viash_version: "0.9.2"
+  viash_version: "0.9.4"
   source: "src"
   target: "target"
   config_mods:
@@ -228,11 +251,13 @@ package_config:
   - ".engines[.type == 'docker'].target_tag := 'save-params'"
   keywords:
   - "bioinformatics"
-  - "sequence"
+  - "sequencing"
   - "high-throughput"
+  - "RNAseq"
   - "mapping"
   - "counting"
   - "pipeline"
+  - "workflow"
   license: "MIT"
   organization: "vsh"
   links:

target/executable/report/create_report/create_report

@@ -2,7 +2,7 @@
 
 # create_report save-params
 # 
-# This wrapper script is auto-generated by viash 0.9.2 and is thus a derivative
+# This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
 # Intuitive.
 # 
@@ -453,6 +453,9 @@ RUN apt-get update && \
   DEBIAN_FRONTEND=noninteractive apt-get install -y procps pandoc && \
   rm -rf /var/lib/apt/lists/*
 
+RUN Rscript -e 'options(warn = 2); install.packages("BiocManager")' && \
+  Rscript -e 'options(warn = 2); BiocManager::install(version = "3.21", type = "source", checkBuilt = TRUE)'
+
 RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")' && \
   Rscript -e 'options(warn = 2); if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' && \
   Rscript -e 'options(warn = 2); if (!requireNamespace("Biobase", quietly = TRUE)) BiocManager::install("Biobase")' && \
@@ -462,9 +465,9 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component report create_report"
-LABEL org.opencontainers.image.created="2025-05-06T14:35:26Z"
+LABEL org.opencontainers.image.created="2025-05-08T12:21:45Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="cc910b428428dd32f183df0c2009fc36e75394e0"
+LABEL org.opencontainers.image.revision="dbca5cbb3a338287f516c79705fc607bcf0905f7"
 LABEL org.opencontainers.image.version="save-params"
 
 VIASHDOCKER

target/executable/report/create_report/nextflow_labels.config

@@ -27,7 +27,7 @@ process {
   withLabel: verylowmem { memory = { get_memory( 4.GB * task.attempt ) } }
   withLabel: lowmem { memory = { get_memory( 8.GB * task.attempt ) } }
   withLabel: midmem { memory = { get_memory( 16.GB * task.attempt ) } }
-  withLabel: highmem { memory = { get_memory( 40.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 64.GB * task.attempt ) } }
 
 }
 

target/executable/report/create_report/plateLayouts.R

@@ -283,15 +283,31 @@ plateLayout <- function(
 
   if (is.null(colours)) {
     colours <- tryCatch({
-      colorRamp2(
+      circlize::colorRamp2(
         breaks = breaks,
         colors = brewer.pal(length(breaks), "Purples")
       )
     },
-    error = function(cond) {
-      return(c("#9370DB", "white"))
+    error = function(cond){
+      
+      message("Recomputed breaks for proper colour mapping")
+      
+      breakValues <- plateValues$values
+      breakValues[which(is.na(breakValues))] <- 0
+      if (all(breakValues >= 0)) {
+        breaks <- computeBreaks(7, max(plateValues$values, na.rm = TRUE))
+      } else {
+        breaks <- quantile(plateValues$values,  probs = seq(0, 1, 0.125))
+      }
+      
+      circlize::colorRamp2(
+        breaks = breaks,
+        colors = brewer.pal(length(breaks), "Purples")
+      )
+      
     })
   }
+  
   ht <- Heatmap(
     plateValues$values,
     column_title = mainTitle, column_title_side = "top",
@@ -425,6 +441,7 @@ computeBreaks <- function(nBreaks, variable) {
     )
     coefExp <- c(exp(coefSystem[1]), coefSystem[2])
     breaks <- coefExp[1] * exp((1:(nBreaks - 1)) * coefExp[2])
+    breaks <- unique(c(0, breaks))
   }
-  return(c(0, breaks))
-}
+  return(breaks)
+}