checkM fails when using Singularity

[Shellfishgene]

Hi!

The first checkM step that defines the root dir does not work when using Singularity as those containers are read only, and that command tries to change a config file. A workaround is using the current biocontainer for checkM quay.io/biocontainers/checkm-genome:1.1.2--py_1, which includes the database. This however breaks the camitaxonomy.py script as the output is slightly different in this version of checkM I think. This in turn can be fixed by skipping lines starting with [ or Bin, for example by changing the code from line 199 onwards like this:

with open(args.checkm) as f:
        next(f)
        for line in f:
            li=line.strip()
            if ( not li.startswith("[") ) and ( not li.startswith("Bin") ):
                (_, name, _, _, _, completeness, contamination, strain_heterogeneity, genome_size, _, _, contigs, _, N50_contigs, _, _, _, _, gc_content, _, coding_density, _, predicted_genes, *_) = line.split('\t')
                sname = name[3:-(len(name)-name.index(" (UID"))]
                checkm_taxon_list.append(getTaxID(sname))