def test_programs(self, data_dir):
     """Identify programs and versions used in analysis.
     """
     from bcbio.provenance import programs
     with make_workdir() as workdir:
         config = load_config(get_post_process_yaml(data_dir, workdir))
         print programs._get_versions(config)

def test_6_bamclean(install_test_files, data_dir):
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, os.pardir, "100326_FC6107FAAXX"),
              os.path.join(data_dir, "run_info-bamclean.yaml")]
        subprocess.check_call(cl)

 def test_1_parallel_vcf_combine(self):
     """Parallel combination of VCF files, split by chromosome.
     """
     from bcbio.variation import vcfutils
     files = [
         os.path.join(self.var_dir, "S1-variants.vcf"),
         os.path.join(self.var_dir, "S2-variants.vcf")
     ]
     with make_workdir() as workdir:
         config = load_config(
             get_post_process_yaml(self.automated_dir, workdir))
         config["algorithm"] = {}
     region_dir = os.path.join(self.var_dir, "S1_S2-combined-regions")
     if os.path.exists(region_dir):
         shutil.rmtree(region_dir)
     if os.path.exists(self.combo_file):
         os.remove(self.combo_file)
     reqs = {"type": "local", "cores": 1}
     with prun.start(reqs, [[config]], config) as run_parallel:
         vcfutils.parallel_combine_variants(
             files, self.combo_file, self.ref_file, config, run_parallel)
     for fname in files:
         if os.path.exists(fname + ".gz"):
             subprocess.check_call(["gunzip", fname + ".gz"])
         if os.path.exists(fname + ".gz.tbi"):
             os.remove(fname + ".gz.tbi")

def test_10_umi(install_test_files, data_dir):
    """Allow BAM files as input to pipeline.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, "run_info-umi.yaml")]
        subprocess.check_call(cl)

def test_7b_cancer_precall(install_test_files, data_dir):
    """Test somatic prioritization and effects prediction with pre-called inputs.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, "run_info-cancer3.yaml")]
        subprocess.check_call(cl)

def test_9_joint(install_test_files, data_dir):
    """Perform joint calling/backfilling/squaring off following variant calling.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, "run_info-joint.yaml")]
        subprocess.check_call(cl)

def test_7_cancer(install_test_files, data_dir):
    """Test paired tumor-normal calling using multiple
    calling approaches: MuTect, VarScan, FreeBayes.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, "run_info-cancer.yaml")]
        subprocess.check_call(cl)

def test_srnaseq_bowtie(install_test_files, data_dir):
    """Run an sRNA-seq analysis.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, os.pardir, "test_srnaseq"),
              os.path.join(data_dir, "run_info-srnaseq_bowtie.yaml")]
        subprocess.check_call(cl)

def test_7_cancer_nonormal(install_test_files, data_dir):
    """Test cancer calling without normal samples or with normal VCF panels.
    Requires MuTect and GATK.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, "run_info-cancer2.yaml")]
        subprocess.check_call(cl)

def test_2_rnaseq(install_test_files, data_dir):
    """Run an RNA-seq analysis with TopHat and generate gene-level counts.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, os.pardir, "110907_ERP000591"),
              os.path.join(data_dir, "run_info-rnaseq.yaml")]
        subprocess.check_call(cl)

def test_3_full_pipeline(install_test_files, data_dir):
    """Run full automated analysis pipeline with multiplexing.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, os.pardir, "110106_FC70BUKAAXX"),
              os.path.join(data_dir, "run_info.yaml")]
        subprocess.check_call(cl)

def test_2_scrnaseq(install_test_files, data_dir):
    """Run a single-cell RNA-seq analysis
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, os.pardir, "Harvard-inDrop"),
              os.path.join(data_dir, "run_info-scrnaseq.yaml")]
        subprocess.check_call(cl)

def test_2_star(install_test_files, data_dir):
    """Run an RNA-seq analysis with STAR and generate gene-level counts.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, os.pardir, "test_fusion"),
              os.path.join(data_dir, "run_info-star.yaml")]
        subprocess.check_call(cl)

def test_2_fastrnaseq(install_test_files, data_dir):
    """Run a fast RNA-seq analysis
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, os.pardir, "test_fusion"),
              os.path.join(data_dir, "run_info-fastrnaseq.yaml")]
        subprocess.check_call(cl)

def test_4_empty_fastq(install_test_files, data_dir):
    """Handle analysis of empty fastq inputs from failed runs.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, os.pardir, "110221_empty_FC12345AAXX"),
              os.path.join(data_dir, "run_info-empty.yaml")]
        subprocess.check_call(cl)

def test_variantcall_2(install_test_files, data_dir):
    """Test variant calling with disambiguation.
    Requires minikraken database.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, os.pardir, "100326_FC6107FAAXX"),
              os.path.join(data_dir, "run_info-variantcall_S3_2.yaml")]
        subprocess.check_call(cl)

def test_detect_fusions_with_ericscipt_with_disambiguate(
        install_test_files, data_dir, setup_logging):
    """Run gene fusion analysis on disambiguated reads with EricScript.
       Requires installation of EricScript and its reference data.
    """
    with make_workdir() as work_dir:
        sample_config = create_sample_config(
            data_dir, work_dir, disambiguate=True)
        ericscript.run(sample_config)
        assert_run_successfully(work_dir=work_dir, data_dir=data_dir)

def test_chipseq(install_test_files, data_dir):
    """
    Run a chip-seq alignment with Bowtie2
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, os.pardir, "test_chipseq"),
              os.path.join(data_dir, "run_info-chipseq.yaml")]
        subprocess.check_call(cl)

def test_1_variantcall(install_test_files, data_dir):
    """Test variant calling with GATK pipeline.
    Requires GATK.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, os.pardir, "100326_FC6107FAAXX"),
              os.path.join(data_dir, "run_info-variantcall.yaml")]
        subprocess.check_call(cl)

def test_fusion(install_test_files, data_dir):
    """Run an RNA-seq analysis and test fusion genes, with human-mouse
    disambiguation.
    Requires minikraken database.
    """
    with make_workdir() as workdir:
        cl = ["bcbio_nextgen.py",
              get_post_process_yaml(data_dir, workdir),
              os.path.join(data_dir, os.pardir, "test_fusion"),
              os.path.join(data_dir, "run_info-fusion_S3.yaml")]
        subprocess.check_call(cl)