Retrieve output files associated with an entire analysis project.

def _get_files_project(sample, upload_config):
    """Retrieve output files associated with an entire analysis project.
    """
    out = [{"path": sample["provenance"]["programs"]}]
    if os.path.exists(tz.get_in(["provenance", "data"], sample) or ""):
        out.append({"path": sample["provenance"]["data"]})
    for fname in ["bcbio-nextgen.log", "bcbio-nextgen-commands.log"]:
        if os.path.exists(os.path.join(log.get_log_dir(sample["config"]), fname)):
            out.append({"path": os.path.join(log.get_log_dir(sample["config"]), fname),
                        "type": "external_command_log",
                        "ext": ""})

    if "summary" in sample and sample["summary"].get("project"):
        out.append({"path": sample["summary"]["project"]})
    if "summary" in sample and sample["summary"].get("metadata"):
        out.append({"path": sample["summary"]["metadata"]})
    mixup_check = tz.get_in(["summary", "mixup_check"], sample)
    if mixup_check:
        out.append({"path": sample["summary"]["mixup_check"],
                    "type": "directory", "ext": "mixup_check"})

    report = os.path.join(dd.get_work_dir(sample), "report")
    if utils.file_exists(report):
        out.append({"path": report,
                    "type": "directory", "ext": "report"})

    multiqc = tz.get_in(["summary", "multiqc"], sample)
    if multiqc:
        out.extend(_flatten_file_with_secondary(multiqc, "multiqc"))

    if sample.get("seqcluster", {}):
        out.append({"path": sample["seqcluster"].get("out_dir"),
                    "type": "directory", "ext": "seqcluster"})

    if sample.get("mirge", {}):
        for fn in sample["mirge"]:
            out.append({"path": fn,
                        "dir": "mirge"})

    if sample.get("report", None):
        out.append({"path": os.path.dirname(sample["report"]),
                    "type": "directory", "ext": "seqclusterViz"})

    for x in sample.get("variants", []):
        if "pop_db" in x:
            out.append({"path": x["pop_db"],
                        "type": "sqlite",
                        "variantcaller": x["variantcaller"]})
    for x in sample.get("variants", []):
        if "population" in x:
            pop_db = tz.get_in(["population", "db"], x)
            if pop_db:
                out.append({"path": pop_db,
                            "type": "sqlite",
                            "variantcaller": x["variantcaller"]})
            suffix = "-annotated-decomposed" if tz.get_in(("population", "decomposed"), x) else "-annotated"
            vcfs = _get_project_vcf(x, suffix)
            out.extend([_add_batch(f, sample) for f in vcfs])
    for x in sample.get("variants", []):
        if x.get("validate") and x["validate"].get("grading_summary"):
            out.append({"path": x["validate"]["grading_summary"]})
            break
    sv_project = set([])
    for svcall in sample.get("sv", []):
        if svcall.get("variantcaller") == "seq2c":
            if svcall.get("calls_all") and svcall["calls_all"] not in sv_project:
                out.append({"path": svcall["coverage_all"], "batch": "seq2c", "ext": "coverage", "type": "tsv"})
                out.append({"path": svcall["read_mapping"], "batch": "seq2c", "ext": "read_mapping", "type": "txt"})
                out.append({"path": svcall["calls_all"], "batch": "seq2c", "ext": "calls", "type": "tsv"})
                sv_project.add(svcall["calls_all"])
    if "coverage" in sample:
        cov_db = tz.get_in(["coverage", "summary"], sample)
        if cov_db:
            out.append({"path": cov_db, "type": "sqlite", "ext": "coverage"})
        all_coverage = tz.get_in(["coverage", "all"], sample)
        if all_coverage:
            out.append({"path": all_coverage, "type": "bed", "ext": "coverage"})

    if dd.get_mirna_counts(sample):
        out.append({"path": dd.get_mirna_counts(sample)})
    if dd.get_isomir_counts(sample):
        out.append({"path": dd.get_isomir_counts(sample)})
    if dd.get_novel_mirna_counts(sample):
        out.append({"path": dd.get_novel_mirna_counts(sample)})
    if dd.get_novel_isomir_counts(sample):
        out.append({"path": dd.get_novel_isomir_counts(sample)})
    if dd.get_combined_counts(sample):
        count_file = dd.get_combined_counts(sample)
        if sample["analysis"].lower() == "scrna-seq":
            out.append({"path": count_file,
                        "type": "mtx"})
            out.append({"path": count_file + ".rownames",
                        "type": "rownames"})
            out.append({"path": count_file + ".colnames",
                        "type": "colnames"})
            out.append({"path": count_file + ".metadata",
                        "type": "metadata"})
            umi_file = os.path.splitext(count_file)[0] + "-dupes.mtx"
            if utils.file_exists(umi_file):
                out.append({"path": umi_file,
                            "type": "mtx"})
                out.append({"path": umi_file + ".rownames",
                            "type": "rownames"})
                out.append({"path": umi_file + ".colnames",
                            "type": "colnames"})
            if dd.get_combined_histogram(sample):
                out.append({"path": dd.get_combined_histogram(sample),
                            "type": "txt"})
            rda = os.path.join(os.path.dirname(count_file), "se.rda")
            if utils.file_exists(rda):
                out.append({"path": rda,
                            "type": "rda"})
        else:
            out.append({"path": dd.get_combined_counts(sample)})
    if dd.get_annotated_combined_counts(sample):
        out.append({"path": dd.get_annotated_combined_counts(sample)})
    if dd.get_combined_fpkm(sample):
        out.append({"path": dd.get_combined_fpkm(sample)})
    if dd.get_combined_fpkm_isoform(sample):
        out.append({"path": dd.get_combined_fpkm_isoform(sample)})
    if dd.get_transcript_assembler(sample):
        out.append({"path": dd.get_merged_gtf(sample)})
    if dd.get_dexseq_counts(sample):
        out.append({"path": dd.get_dexseq_counts(sample)})
        out.append({"path": "%s.ann" % dd.get_dexseq_counts(sample)})
    if dd.get_express_counts(sample):
        out.append({"path": dd.get_express_counts(sample)})
    if dd.get_express_fpkm(sample):
        out.append({"path": dd.get_express_fpkm(sample)})
    if dd.get_express_tpm(sample):
        out.append({"path": dd.get_express_tpm(sample)})
    if dd.get_isoform_to_gene(sample):
        out.append({"path": dd.get_isoform_to_gene(sample)})
    if dd.get_square_vcf(sample):
        out.append({"path": dd.get_square_vcf(sample)})
    if dd.get_sailfish_transcript_tpm(sample):
        out.append({"path": dd.get_sailfish_transcript_tpm(sample)})
    if dd.get_sailfish_gene_tpm(sample):
        out.append({"path": dd.get_sailfish_gene_tpm(sample)})
    if dd.get_tx2gene(sample):
        out.append({"path": dd.get_tx2gene(sample)})
    if dd.get_spikein_counts(sample):
        out.append({"path": dd.get_spikein_counts(sample)})
    transcriptome_dir = os.path.join(dd.get_work_dir(sample), "inputs",
                                     "transcriptome")
    if os.path.exists(transcriptome_dir):
        out.append({"path": transcriptome_dir, "type": "directory",
                    "ext": "transcriptome"})
    return _add_meta(out, config=upload_config)