Merge pull request #97 from AlexsLemonade/allyhawkins/add-filtering-m…

…etadata Add filtering method to metadata.json
AlexsLemonade · Feb 14, 2022 · 1ef2286 · 1ef2286
2 parents 036b0af + 63371ec
commit 1ef2286
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diff --git a/bin/sce_qc_report.R b/bin/sce_qc_report.R
@@ -106,6 +106,7 @@ filtered_sce <- readr::read_rds(opt$filtered_sce)
 
 # Compile metadata for output files
 sce_meta <- metadata(unfiltered_sce)
+filtered_sce_meta <- metadata(filtered_sce)
 
 # check for alt experiments (CITE-seq, etc)
 alt_expts <- altExpNames(unfiltered_sce)
@@ -119,6 +120,7 @@ metadata_list <- list(
   has_citeseq = has_citeseq,
   filtered_cells = ncol(filtered_sce),
   unfiltered_cells = ncol(unfiltered_sce),
+  filtering_method = filtered_sce_meta$filtering_method,
   total_reads = sce_meta$total_reads,
   mapped_reads = sce_meta$mapped_reads,
   genome_assembly = opt$genome_assembly,

diff --git a/config/containers.config b/config/containers.config
@@ -1,5 +1,5 @@
 // Docker container images
-SCPCATOOLS_CONTAINER = 'ghcr.io/alexslemonade/scpca-tools:v0.1.3'
+SCPCATOOLS_CONTAINER = 'ghcr.io/alexslemonade/scpca-tools:edge'
 
 SALMON_CONTAINER = 'quay.io/biocontainers/salmon:1.5.2--h84f40af_0'
 ALEVINFRY_CONTAINER = 'quay.io/biocontainers/alevin-fry:0.4.2--h7d875b9_0'