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Changed to saveRDS instead of save
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jenzopr committed Jun 18, 2018
1 parent 5850d05 commit ebea9e7
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Showing 5 changed files with 6 additions and 6 deletions.
2 changes: 1 addition & 1 deletion config/default.yml
Original file line number Diff line number Diff line change
Expand Up @@ -149,7 +149,7 @@ dirs:
quant: 'quant'
tables: 'tables'
log: 'log'
R: 'RData'
R: 'rds'

#
# The debug section
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2 changes: 1 addition & 1 deletion sc-preprocess.snake
Original file line number Diff line number Diff line change
Expand Up @@ -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 :-) ------------------------------------#
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4 changes: 2 additions & 2 deletions src/container.snake
Original file line number Diff line number Diff line change
Expand Up @@ -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')
Expand All @@ -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')
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2 changes: 1 addition & 1 deletion src/createSCE_kallisto.R
Original file line number Diff line number Diff line change
Expand Up @@ -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)
2 changes: 1 addition & 1 deletion src/createSCE_salmon.R
Original file line number Diff line number Diff line change
Expand Up @@ -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)

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