Prepare a set of configuration items for input files.

def _prep_items_from_base(base, in_files, metadata, separators, force_single=False):
    """Prepare a set of configuration items for input files.
    """
    details = []
    in_files = _expand_dirs(in_files, KNOWN_EXTS)
    in_files = _expand_wildcards(in_files)

    ext_groups = collections.defaultdict(list)
    for ext, files in itertools.groupby(
            in_files, lambda x: KNOWN_EXTS.get(utils.splitext_plus(x)[-1].lower())):
        ext_groups[ext].extend(list(files))
    for ext, files in ext_groups.items():
        if ext == "bam":
            for f in files:
                details.append(_prep_bam_input(f, base))
        elif ext in ["fastq", "fq", "fasta"]:
            files, glob_files = _find_glob_matches(files, metadata)
            for fs in glob_files:
                details.append(_prep_fastq_input(fs, base))
            for fs in fastq.combine_pairs(files, force_single, separators=separators):
                details.append(_prep_fastq_input(fs, base))
        elif ext in ["vcf"]:
            for f in files:
                details.append(_prep_vcf_input(f, base))
        else:
            print("Ignoring unexpected input file types %s: %s" % (ext, list(files)))
    return details