<commit_before>################################################################
#
#
# Pipeline pipeline_@template@.py configuration file for sphinxreport
#
# 
################################################################
## general options
[general]

# the genome to use
genome=hg19

# directory where exported data is located
exportdir=export

# location of indexed genome 
genome_dir=/ifs/mirror/genomes/plain

# name of database
database=csvdb

# database options for csv2db script
csv2db_options=--backend=sqlite --retry --map=gene_id:str --map=contig:str --map=transcript_id:str 

# scratchdir for data not to be backed up
scratchdir=/tmp

# a version string
version=

################################################################
#
# Location of annotation database
#
################################################################
[annotations]
database=/ifs/data/annotations/hg19_ensembl62/csvdb

# directory with annotation information
dir=/ifs/data/annotations/hg19_ensembl62

################################################################
#
# sphinxreport build options
#
################################################################
[report]
# number of threads to use to build the documentation
threads=10

# directory for html documentation
html=report/html

# directory for doctrees
doctrees=report/doctrees

<commit_msg>pipeline_quickstart - rename publish_report to publish<commit_after>################################################################
#
#
# Pipeline pipeline_@template@.py configuration file for sphinxreport
#
# 
################################################################
## general options
[general]

# the genome to use
genome=hg19

# directory where exported data is located
exportdir=export

# location of indexed genome 
genome_dir=/ifs/mirror/genomes/plain

# name of database
database=csvdb

# database options for csv2db script
csv2db_options=--backend=sqlite --retry --map=gene_id:str --map=contig:str --map=transcript_id:str 

# scratchdir for data not to be backed up
scratchdir=/tmp

# directory for publishing on the web
web_dir=../web

# a version string
version=

################################################################
#
# Location of annotation database
#
################################################################
[annotations]
database=/ifs/data/annotations/hg19_ensembl62/csvdb

# directory with annotation information
dir=/ifs/data/annotations/hg19_ensembl62

################################################################
#
# sphinxreport build options
#
################################################################
[report]
# number of threads to use to build the documentation
threads=10

# directory for html documentation
html=report/html

# directory for doctrees
doctrees=report/doctrees


{'fraction_non_alphanumeric': 0.3353636689358653, 'fraction_numerical': 0.01003224650662845, 'mean_word_length': 7.28486646884273, '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': '7242541', 'n_tokens_mistral': 732, 'n_tokens_neox': 652, 'n_words': 187}