<commit_before>#!/bin/bash
if [ -z pipeline_stats.ipynb ];
then
	echo "You should run the pipeline stats before cleaning the tmp files"
	exit 1
fi

#Remove tmp folder
rm -r tmp/

#Remove temporary qf files
find 2_qf -name "*.fq.gz" -delete

#Remove
rm 3_hostfiltering/*.fq

#Remove assembler-specific folders
rm -r 4_assembly/fermi
rm -r 4_assembly/megahit
rm -r 4_assembly/spades

#Remove tmp mapping files to determine non-incorporated reads
rm 4_assembly/singletons/*.sam<commit_msg>Add -r flag to delete the Spades asm folder<commit_after>#!/bin/bash
if [ -z pipeline_stats.ipynb ];
then
	echo "You should run the pipeline stats before cleaning the tmp files"
	exit 1
fi

#Remove tmp folder
rm -r tmp/

#Remove temporary qf files
find 2_qf -name "*.fq.gz" -delete

#Remove
rm 3_hostfiltering/*.fq

#Remove assembler-specific folders
rm -r 4_assembly/fermi
rm -r 4_assembly/megahit
rm -rf 4_assembly/spades

#Remove tmp mapping files to determine non-incorporated reads
rm 4_assembly/singletons/*.sam
{'fraction_non_alphanumeric': 0.08673978065802593, 'fraction_numerical': 0.013958125623130608, 'mean_word_length': 4.229166666666667, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '7289755', 'n_tokens_mistral': 376, 'n_tokens_neox': 345, 'n_words': 127}