README.md

bactos.nf

conda/process_fastp.yml

conda/process_fastqc.yml

conda/process_hisat2.yml

conda/process_multiqc.yml

conda/process_stringtie.yml

conda/process_trimmomatic.yml

config/compute_resources.config

config/multiqc_conf.yml

config/software_packages.config

config/test_profile.config

containers/hisat2/Dockerfile

...scherichia_coli_gca_001606525.ASM160652v1.dna.toplevel.fa

data/bakta_db/db.tar.gz

nextflow.config

pipeline_report/execution_report.html

pipeline_report/execution_report.html.1

pipeline_report/execution_timeline.html

pipeline_report/execution_timeline.html.1