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CheckM

note

CheckM estimates genome completeness and contamination based on the presence or absence of marker genes

https://github.com/Ecogenomics/CheckM

The module parses the output files generated by CheckM. It will only parse an output file from checkm lineage_wf, checkm taxonomy_wf, and checkm qa. The output file needs to be in format 1 (-o 1). All statistics for all samples are saved to multiqc_data/checkm-table.txt.

This has been tested with CheckM v1.2.1 .

File search patterns​

checkm:
  - contents_re: ".*Bin Id(?:\t| {3,})Marker lineage(?:\t| {3,})# genomes(?:\t| {3,})#\
      \ markers(?:\t| {3,})# marker sets.*"
    num_lines: 10