Small bug fixes

jenzopr · Apr 30, 2018 · d5d77b7 · d5d77b7
1 parent 1f380e1
commit d5d77b7
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Showing 3 changed files with 6 additions and 3 deletions.
diff --git a/environment.yml b/environment.yml
@@ -9,7 +9,7 @@ dependencies:
   - salmon
   - kallisto
   #- htstream
-  #- umis
+  - umis
   - r-magrittr
   - r-data.table
   - r-readr

diff --git a/src/auxiliary.snake b/src/auxiliary.snake
@@ -27,7 +27,10 @@ def find_nested_key(d, k):
   return(None)
 
 def find_metadata_files(wildcards):
-  metadata = [config['samplesheet']['file'], join(config['dirs']['tables'], 'salmon.txt')]
+  metadata = [config['samplesheet']['file']]
+  if config['action']['quantification'] == 'salmon':
+    metadata.extend([config['samplesheet']['file'], join(config['dirs']['tables'], 'salmon.txt')])
+
   if config['action']['clean']:
     metadata.extend([join(config['dirs']['tables'], 'htstream.txt')])
   if config['action']['demultiplex']:

diff --git a/src/createSCE_kallisto.R b/src/createSCE_kallisto.R
@@ -66,7 +66,7 @@ if (!is.null(metadata_files)) {
   metadata_ <- lapply(metadata_files, function(p) metadata <- data.table::fread(input = p, sep = "\t", header = T, stringsAsFactors = T, na.strings = "NA"))
   metadata <- Reduce(function(a, b) dplyr::left_join(a, b, by = snakemake@config$samplesheet$index), metadata_)
 
-  m <- match(colnames(expression[[1]]), make.names(metadata[, snakemake@config$samplesheet$index]))
+  m <- match(colnames(expression[[1]]), make.names(metadata[[which(colnames(metadata) == snakemake@config$samplesheet$index)]]))
   colData_ <- as.data.frame(metadata[na.omit(m), ])
   rownames(colData_) <- make.names(colData_[, snakemake@config$samplesheet$index])
 } else {