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keep log file list in local workdir rather than global to avoid singu…
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…larity file permission issues
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David Ladd committed Jan 17, 2023
1 parent 072a40b commit 6867001
Showing 1 changed file with 1 addition and 5 deletions.
6 changes: 1 addition & 5 deletions modules/local/enchantr/report_file_size.nf
Original file line number Diff line number Diff line change
Expand Up @@ -21,12 +21,8 @@ process REPORT_FILE_SIZE {
path "file_size_report/tables/log_data.tsv", emit: table

script:
def all_logs = logs.join('\n')
def logs_file = workDir + '/logs.txt'
logs_file = file(logs_file)
logs_file.text = all_logs
"""
mv "${logs_file}" .
echo "${logs.join('\n')}" > logs.txt
Rscript -e "enchantr::enchantr_report('file_size', \\
report_params=list('input'='logs.txt', 'metadata'='${metadata}',\\
'outdir'=getwd()))"
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