Fix seurat obj not found (#71)

* Sample ids property sent as list instead of string * fix seurat_obj not found Co-authored-by: Martin Fosco <[email protected]> Co-authored-by: Oliver Gibson <[email protected]> Co-authored-by: Xavier Verges <[email protected]>
hms-dbmi-cellenics · May 27, 2021 · 7e93f2d · 7e93f2d
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diff --git a/pipeline-runner/src/data-ingest/4_Prepare_experiment.r b/pipeline-runner/src/data-ingest/4_Prepare_experiment.r
@@ -96,7 +96,7 @@ add_custom_config_per_sample <- function(step_fn, config, scdata){
   # We upadte the config file, so to be able to access the raw config we create a copy
   config.raw <- config
 
-  samples <- seurat_obj$samples
+  samples <- scdata$samples
 
   for(sample in unique(samples)){
     # Downsample the seurat object to a unisample experiment

diff --git a/pipeline-runner/src/data-ingest/5_Upload-to-aws.r b/pipeline-runner/src/data-ingest/5_Upload-to-aws.r
@@ -15,7 +15,7 @@ create_samples_table <- function(config, experiment_id, project_id) {
                              row.names = 'samples')
 
   samples <- row.names(df_prefiltered)
-  samples_table$ids = paste0("sample-", samples)
+  samples_table$ids <- lapply(samples, function(x) paste0("sample-", x, sep = ""))
 
   # For the current datasets it could happen that they are not in the gz format, so we leave the alternative tsv format.
   mime_options = c(