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Solve the following problem using Python, implementing the functions described below, one line at a time
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Description:
 def variant(samples):
 """Variant calling workflow definition for CWL generation. """

    checkpoints = _variant_checkpoints(samples)
    if checkpoints["align"]:
        align_wf = _alignment(checkpoints)
        alignin = [["files"], ["analysis"],
                   ["config", "algorithm", "align_split_size"],
                   ["reference", "fasta", "base"],
                   ["rgnames", "pl"], ["rgnames", "sample"], ["rgnames", "pu"],
                   ["rgnames", "lane"], ["rgnames", "rg"], ["rgnames", "lb"],
                   ["reference", "aligner", "indexes"],
                   ["config", "algorithm", "aligner"],
                   ["config", "algorithm", "trim_reads"],
                   ["config", "algorithm", "adapters"],
                   ["config", "algorithm", "bam_clean"],
                   ["config", "algorithm", "variant_regions"],
                   ["config", "algorithm", "mark_duplicates"]]
        if checkpoints["hla"]:
            alignin.append(["config", "algorithm", "hlacaller"])
        if checkpoints["umi"]:
            alignin.append(["config", "algorithm", "umi_type"])
        align = [s("alignment_to_rec", "multi-combined", alignin,
                   [cwlout("alignment_rec", "record")],
                   "bcbio-vc",
                   disk={"files": 1.5}, cores=1, no_files=True),
                 w("alignment", "multi-parallel", align_wf,
                   [["align_split"], ["process_alignment_rec"],
                    ["work_bam"], ["config", "algorithm", "quality_format"]])]
    else:
        align = [s("organize_noalign", "multi-parallel",
                   ["files"],
                   [cwlout(["align_bam"], ["File", "null"], [".bai"]),
                    cwlout(["work_bam_plus", "disc"], ["File", "null"]),
                    cwlout(["work_bam_plus", "sr"], ["File", "null"]),
                    cwlout(["hla", "fastq"], ["File", "null"])],
                   "bcbio-vc", cores=1)]
    align_out = [["rgnames", "sample"], ["align_bam"]]
    pp_align, pp_align_out = _postprocess_alignment(checkpoints)
    if checkpoints["umi"]:
        align_out += [["umi_bam"]]
    vc, vc_out = _variant_vc(checkpoints)
    sv, sv_out = _variant_sv(checkpoints)
    hla, hla_out = _variant_hla(checkpoints)
    qc, qc_out = _qc_workflow(checkpoints)
    steps = align + pp_align + hla + vc + sv + qc
    final_outputs = align_out + pp_align_out + vc_out + hla_out + sv_out + qc_out
    return steps, final_outputs