<commit_before>bcbio_nextgen.py -w template bcbio.yaml bcbio.csv *.fastq.gz

cd bcbio/work

# slurm
cp ../../sbatch_bcbio.sh .
sbatch sbatch_bcbio.sh
squeue -u $USER

less *.err
tree
<commit_msg>Update bcbio template script<commit_after>bcbio_nextgen.py -w template bcbio.yaml bcbio.csv *.fastq.gz

cd bcbio/work

# slurm
ln -s ../../sbatch_bcbio.sh .
sbatch sbatch_bcbio.sh
squeue -u $USER
sshare -U
# sprio -j JOBID
# less *.err
# tree

{'fraction_non_alphanumeric': 0.1278538812785388, 'fraction_numerical': 0.0, 'mean_word_length': 3.4343434343434343, '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': '3726217', 'n_tokens_mistral': 199, 'n_tokens_neox': 194, 'n_words': 47}