Minimap2 issue with map-hifi

[ivwonter]

Please leave the headers below and replace the relevant text. This will expedite addressing the ticket.

Name the workflow HiFi-MAG-Pipeline

Describe the bug Older version of minimap2 (v2.17-r941) in conda environment does not seem to be compatible with the '-x mag-hifi' preset causing the pipeline to fail. Recommend changing the version of minimap2 to the latest release (anything from v2.22 onwards).

Expected behavior Expected pipeline and mapping to run as normal

Screenshots Activating conda environment: .snakemake/conda/6449c2824f4382d1b8f2a13dc4e35f69_ [Fri Sep 22 16:01:04 2023] Error in rule MinimapIndex: jobid: 22 input: ... output: ... log: ... conda-env: ... shell: minimap2 -x map-hifi -t 20 -d ... (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!) Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2023-09-22T160100.152624.snakemake.log

Log files [ERROR] unknown preset 'map-hifi'

[baotg080599]

name: samtools_env channels:

• bioconda
• conda-forge
• defaults dependencies:
• samtools == 1.10
• minimap2

paste this overwrite into samtools.yml

[dportik]

Thanks for highlighting the issue, it was resolved in #70