Changed to saveRDS instead of save

jenzopr · Jun 18, 2018 · ebea9e7 · ebea9e7
1 parent 5850d05
commit ebea9e7
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Showing 5 changed files with 6 additions and 6 deletions.
diff --git a/config/default.yml b/config/default.yml
@@ -149,7 +149,7 @@ dirs:
   quant: 'quant'
   tables: 'tables'
   log: 'log'
-  R: 'RData'
+  R: 'rds'
 
 #
 # The debug section

diff --git a/sc-preprocess.snake b/sc-preprocess.snake
@@ -52,7 +52,7 @@ elif config['action']['quantification'] == 'kallisto':
 	output_files.extend([join(config['dirs']['quant'], 'run_info.json')])
 
 if config['action']['container']:
-	output_files.extend([join(config['dirs']['R'], 'scData.Rdata')])
+	output_files.extend([join(config['dirs']['R'], 'scData.rds')])
 
 #-------------------------------------------------------------------------------#
 #---------------------------------- RUN :-) ------------------------------------#

diff --git a/src/container.snake b/src/container.snake
@@ -14,7 +14,7 @@ if config['action']['quantification'] == 'salmon':
       metadata = find_metadata_files,
       quant_files = expand('{o}/{s}/quant.sf', o = config['dirs']['quant'], s = SAMPLE_NAMES)
     output:
-      rdata = join(config['dirs']['R'], 'scData.Rdata')
+      rdata = join(config['dirs']['R'], 'scData.rds')
     params:
       samples = SAMPLE_NAMES,
       colData = samplesheet.ix[SAMPLE_NAMES].to_dict(orient = 'list')
@@ -30,7 +30,7 @@ elif config['action']['quantification'] == 'kallisto':
       tx2gene = join(config['dirs']['ref'], 'tx2gene', basename(REFERENCE_FASTA).rstrip(".fa")),
       metadata = find_metadata_files
     output:
-      rdata = join(config['dirs']['R'], 'scData.Rdata')
+      rdata = join(config['dirs']['R'], 'scData.rds')
     params:
       samples = SAMPLE_NAMES,
       colData = samplesheet.ix[SAMPLE_NAMES].to_dict(orient = 'list')

diff --git a/src/createSCE_kallisto.R b/src/createSCE_kallisto.R
@@ -89,4 +89,4 @@ if (is.null(rowData_) & !is.null(colData_)) {
 #
 # Save generated object
 #
-save(scData, file = snakemake@output$rdata)
+saveRDS(scData, file = snakemake@output$rdata)
diff --git a/src/createSCE_salmon.R b/src/createSCE_salmon.R
@@ -87,4 +87,4 @@ if (is.null(rowData_) & !is.null(colData_)) {
 #
 # Save generated object
 #
-save(scData, file = snakemake@output$rdata)
+saveRDS(scData, file = snakemake@output$rdata)