.gitignore

*~
\#*
*.o
OPERA-LG/bin/OPERA-LG
SIGMA/sigma.config
bin/bundler
bin/sigma
bin/short_read_analysis
complete_ref_genomes/
database_updated
genomeDB_Sketch.msh
utils/MUMmer3.23/
utils/download
utils/tmp_module.str
OPERA-LG/bin/OPERA-LG-fast
OPERA-LG/bin/get_paf_file.pl
OPERA-MS-1.1
SIGMA/debug
bin/OPERA-LG-fast
database_updated.bk
utils/perl
__pycache__
utils_db/minikraken2_v2_8GB
TLL*/
utils
utils_db
test_novel
#Some software that are not ready to be added
#utils/metabat
#utils/jgi_summarize_bam_contig_depths
#utils/clustering.r
#utils/novel_analysis.py
#bin/novel_analysis.py
#utils_db
#utils_db/*
tools_opera_ms/perl
tools_opera_ms/maxbin2

#utils/kraken2
tools_opera_ms/maxbin
tools_opera_ms/checkm
tools_opera_ms/MUMmer3.23

src_utils_denis/
OPERA-MS-DB*
minikraken_8GB*
#OPERA-MS-UTILS.py
OPERA-LG/bin/.#OPERA-long-read.pl
genomes_lists.txt.tar.gz
log.err

#For the test files
test_files/OPERA_MS*/
test_files/sample_output/
test_files/OUT/
test_files/RESULTS/
test_files/log.err
test_files/OPERA-MS-LOG.tar.gz
test_files/fna_output/
test_files/OUTFILE.fa
test_files/fasta_log.err
test_files/fasta_results/
test_files/run.log
test_files/SINGLE/
test_files/log.txt
test_files/RESULTS_NO_REF/