AMR++ is a bioinformatic pipeline meant to aid in the analysis of raw sequencing reads to characterize the profile of antimicrobial resistance genes, or resistome.
With the current version of multiqc the report html and data directory include the config title (taken from data/multiqc/multiqc_config.yaml) in their path, i.e.:
multiqc_data/ -> AMR-Bioinformatic-pipeline_multiqc_report_data
and
multiqc_report.html -> AMR-Bioinformatic-pipeline_multiqc_report.html
This PR tells multiqc to use the filename multiqc_report instead of including the config title in the names, and moves everything in a similar place as before.
@EnriqueDoster Let me know if you'd like it better if the multiqc version is getting fixed to 1.6 as mentioned in the docpage here. I could then close this PR and open a new one fixing the version in the env-file here envs/AMR++_env.yaml#L9
This aims to fix #31
With the current version of
multiqcthe report html and data directory include the config title (taken fromdata/multiqc/multiqc_config.yaml) in their path, i.e.:This PR tells multiqc to use the filename
multiqc_reportinstead of including the config title in the names, and moves everything in a similar place as before.@EnriqueDoster Let me know if you'd like it better if the multiqc version is getting fixed to 1.6 as mentioned in the docpage here. I could then close this PR and open a new one fixing the version in the env-file here envs/AMR++_env.yaml#L9