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extraneous_file_finder.sh
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extraneous_file_finder.sh
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Folders you can most likely delete, which contain extra files and snakemake logs
find . -print0 > find_tmp.txt
echo "# finding likely extra directories" > extra_files.txt
echo "# .snakemake folders" >> extra_files.txt
# .snakemake directories
grep "\.snakemake$" find_tmp.txt >> extra_files.txt
# Spades assembly temp files and graphs
echo "# extra spades assembly directories" >> extra_files.txt
grep "spades.*K[0-9][0-9]$" find_tmp.txt >> extra_files.txt
grep "spades.*misc$" find_tmp.txt >> extra_files.txt
grep "spades.*corrected$" find_tmp.txt >> extra_files.txt
grep "spades.*tmp$" find_tmp.txt >> extra_files.txt
# Megahit assembly temp files and graphs
echo "# extra megahit assembly directories" >> extra_files.txt
grep "megahit.*intermediate_contigs" find_tmp.txt >> extra_files.txt
# preprocessing extra files
echo "# extra preprocessing files" >> extra_files.txt
grep "preprocessing.*01_trimmed.*.fq.gz$" find_tmp.txt >> extra_files.txt
grep "preprocessing.*02_dereplicate.*fastq$" find_tmp.txt >> extra_files.txt
grep "preprocessing.*03_sync.*fq$" find_tmp.txt >> extra_files.txt
grep "preprocessing.*04_.*fq$" find_tmp.txt >> extra_files.txt