Merge pull request #730 from AlexsLemonade/allyhawkins/v0.8.0-bug-hun…

…ting Fix bugs in v0.8.0
AlexsLemonade · Mar 15, 2024 · 8bef82d · 8bef82d
2 parents 246c3d7 + ea2edcb
commit 8bef82d
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Showing 4 changed files with 7 additions and 8 deletions.
diff --git a/bin/generate_unfiltered_sce.R b/bin/generate_unfiltered_sce.R
@@ -200,7 +200,7 @@ sample_type <- sample_metadata_df |>
       is_xenograft ~ "patient-derived xenograft",
       is_cell_line ~ "cell line",
       # if neither column was provided, note that
-      is.na(is_xenograft) && is.na(is_cell_line) ~ "Not provided",
+      is.na(is_xenograft) & is.na(is_cell_line) ~ "Not provided",
       .default = "patient tissue"
     )
   ) |>

diff --git a/modules/af-rna.nf b/modules/af-rna.nf
@@ -56,7 +56,7 @@ process alevin_rad {
 process fry_quant_rna {
   container params.ALEVINFRY_CONTAINER
   label 'cpus_8'
-  label 'mem_8'
+  label 'mem_16'
   tag "${meta.run_id}-rna"
   publishDir "${params.checkpoints_dir}/alevinfry/${meta.library_id}", mode: 'copy', enabled: params.publish_fry_outs
 

diff --git a/modules/qc-report.nf b/modules/qc-report.nf
@@ -3,7 +3,7 @@
 
 process sce_qc_report {
   container params.SCPCATOOLS_CONTAINER
-  label 'mem_8'
+  label 'mem_16'
   tag "${meta.library_id}"
   publishDir "${params.results_dir}/${meta.project_id}/${meta.sample_id}", mode: 'copy'
   input:

diff --git a/templates/qc_report/main_qc_report.rmd b/templates/qc_report/main_qc_report.rmd
@@ -526,13 +526,12 @@ if (skip_miQC) {
     miQC_plot <- miQC::plotMetrics(filtered_sce)
   } else {
     miQC_plot <- miQC::plotModel(filtered_sce, model = miQC_model)
+    # set line thickness
+    line_aes <- list(linewidth = 1, alpha = 0.8)
+    miQC_plot$layers[[2]]$aes_params <- line_aes
+    miQC_plot$layers[[3]]$aes_params <- line_aes
   }
 
-  # set line thickness
-  line_aes <- list(linewidth = 1, alpha = 0.8)
-  miQC_plot$layers[[2]]$aes_params <- line_aes
-  miQC_plot$layers[[3]]$aes_params <- line_aes
-
   miQC_plot +
     coord_cartesian(ylim = c(0, 100)) +
     scale_x_continuous(labels = scales::label_number(accuracy = 1)) +