From ebea9e7eb2f51b142bf166a455e962fb3bfc6a83 Mon Sep 17 00:00:00 2001
From: Jens Preussner <jens.preussner@mpi-bn.mpg.de>
Date: Mon, 18 Jun 2018 17:48:11 +0200
Subject: [PATCH] Changed to saveRDS instead of save

---
 config/default.yml       | 2 +-
 sc-preprocess.snake      | 2 +-
 src/container.snake      | 4 ++--
 src/createSCE_kallisto.R | 2 +-
 src/createSCE_salmon.R   | 2 +-
 5 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/config/default.yml b/config/default.yml
index 5295807..4a9eab5 100644
--- 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
index 49aa446..f952ce7 100644
--- 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
index 75bf483..0bb0fd5 100644
--- 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
index 63dc24b..5f525b7 100644
--- 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
index 5731215..4af9c6f 100644
--- 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)