diff --git a/tests/test_cli_run.py b/tests/test_cli_run.py
deleted file mode 100644
index 61ecb40..0000000
--- a/tests/test_cli_run.py
+++ /dev/null
@@ -1,200 +0,0 @@
-"""This does not cover all CLI parameters defined in caper/caper_args.py.
-Google Cloud Platform is tested in test_cli_server_client.py.
-However, other cloud (aws) and HPCs (slurm/sge/pbs) are not tested.
-
-In this testing module, 'caper run' is tested with a local backend.
-
-See test_cli_server_client.py for 'caper server/submit/...'.
-We will use gcp (Google Cloud Platform) backend to test server-client
-functions.
-"""
-import json
-import os
-
-import pytest
-from autouri import GCSURI
-
-from caper.cli import main as cli_main
-from caper.cromwell_metadata import CromwellMetadata
-from caper.wdl_parser import WDLParser
-
-from .example_wdl import make_directory_with_wdls
-
-
-def test_wrong_subcmd():
-    cmd = ['wrong_subcmd']
-    with pytest.raises(SystemExit):
-        cli_main(cmd)
-
-
-@pytest.mark.parametrize(
-    'cmd',
-    [
-        ['--docker', '--singularity'],
-        ['--docker', 'ubuntu:latest', '--singularity'],
-        ['--docker', '--singularity', 'docker://ubuntu:latest'],
-        ['--docker', 'ubuntu:latest', '--singularity', 'docker://ubuntu:latest'],
-        ['--docker', '--soft-glob-output'],
-        ['--docker', 'ubuntu:latest', '--soft-glob-output'],
-    ],
-)
-def test_mutually_exclusive_params(tmp_path, cmd):
-    make_directory_with_wdls(str(tmp_path))
-
-    cmd = ['run', str(tmp_path / 'main.wdl')] + cmd
-    with pytest.raises(ValueError):
-        cli_main(cmd)
-
-
-@pytest.mark.integration
-def test_run(tmp_path, cromwell, womtool, debug_caper):
-    """Will test most local parameters (run only) here."""
-    make_directory_with_wdls(str(tmp_path))
-    wdl = tmp_path / 'main.wdl'
-    inputs = tmp_path / 'inputs.json'
-    p = WDLParser(str(wdl))
-    imports = p.zip_subworkflows(str(tmp_path / 'imports.zip'))
-
-    cmd = ['run']
-    cmd += [str(wdl)]
-    cmd += ['--tmp-dir', str(tmp_path / 'tmp_dir')]
-    # local (instead of correct Local with capital L) should work.
-    cmd += ['--backend', 'local']
-    cmd += ['--cromwell-stdout', str(tmp_path / 'cromwell_stdout.o')]
-    cmd += ['--db', 'file']
-    cmd += ['--db-timeout', '500000']
-    cmd += ['--file-db', str(tmp_path / 'file_db_prefix')]
-    cmd += ['--max-concurrent-tasks', '2']
-    cmd += ['--max-concurrent-workflows', '2']
-    cmd += ['--disable-call-caching']
-    cmd += ['--soft-glob-output']
-    cmd += ['--local-hash-strat', 'path']
-    cmd += ['--local-out-dir', str(tmp_path / 'out_dir')]
-    cmd += ['--inputs', str(inputs)]
-    cmd += ['--imports', str(imports)]
-    cmd += ['--ignore-womtool']
-    cmd += ['--cromwell', cromwell]
-    cmd += ['--womtool', womtool]
-    cmd += ['--java-heap-womtool', '2G']
-    cmd += ['--java-heap-run', '2G']
-    cmd += ['--max-retries', '1']
-    cmd += ['--metadata-output', str(tmp_path / 'metadata.json')]
-    if debug_caper:
-        cmd += ['--debug']
-
-    cli_main(cmd)
-
-    assert (tmp_path / 'tmp_dir').exists()
-    assert (tmp_path / 'file_db_prefix.lobs').exists()
-    assert (tmp_path / 'metadata.json').exists()
-    assert (tmp_path / 'cromwell_stdout.o').exists()
-
-    # test cleanup() on local storage
-    cm = CromwellMetadata(str(tmp_path / 'metadata.json'))
-    # check if metadata JSON and workflowRoot dir exists
-    root_out_dir = cm.data['workflowRoot']
-    assert os.path.exists(root_out_dir) and os.path.isdir(root_out_dir)
-
-    # dry-run should not delete anything
-    cm.cleanup(dry_run=True)
-    assert os.path.exists(root_out_dir)
-
-    cm.cleanup(dry_run=False)
-    assert not os.path.exists(root_out_dir)
-
-
-@pytest.mark.google_cloud
-@pytest.mark.integration
-def test_run_gcp_with_life_sciences_api(
-    tmp_path,
-    gcs_root,
-    ci_prefix,
-    cromwell,
-    womtool,
-    gcp_prj,
-    gcp_service_account_key_json,
-    debug_caper,
-):
-    """Test run with Google Cloud Life Sciences API"""
-    out_gcs_bucket = os.path.join(gcs_root, 'caper_out', ci_prefix)
-    tmp_gcs_bucket = os.path.join(gcs_root, 'caper_tmp')
-
-    # prepare WDLs and input JSON, imports to be submitted
-    make_directory_with_wdls(str(tmp_path))
-    wdl = tmp_path / 'main.wdl'
-    inputs = tmp_path / 'inputs.json'
-    metadata = tmp_path / 'metadata.json'
-
-    cmd = ['run', str(wdl)]
-    cmd += ['--inputs', str(inputs)]
-    cmd += ['-m', str(metadata)]
-    if gcp_service_account_key_json:
-        cmd += ['--gcp-service-account-key-json', gcp_service_account_key_json]
-    cmd += ['--gcp-region', 'us-central1']
-    cmd += ['--gcp-zones', 'us-west1-a,us-west1-b']
-    cmd += ['--gcp-prj', gcp_prj]
-    cmd += ['--memory-retry-error-keys', 'Killed']
-    cmd += ['--memory-retry-multiplier', '1.5']
-    cmd += ['--tmp-dir', str(tmp_path / 'tmp_dir')]
-    cmd += ['--backend', 'gcp']
-    cmd += ['--gcp-out-dir', out_gcs_bucket]
-    cmd += ['--gcp-loc-dir', tmp_gcs_bucket]
-    cmd += ['--cromwell-stdout', str(tmp_path / 'cromwell_stdout.o')]
-    # test with file type DB
-    cmd += ['--db', 'file']
-    cmd += ['--db-timeout', '500000']
-    cmd += ['--file-db', str(tmp_path / 'file_db_prefix')]
-    cmd += ['--max-concurrent-tasks', '2']
-    cmd += ['--max-concurrent-workflows', '2']
-    cmd += ['--disable-call-caching']
-    cmd += ['--cromwell', cromwell]
-    cmd += ['--womtool', womtool]
-    cmd += ['--java-heap-run', '4G']
-    cmd += ['--docker', 'ubuntu:latest']
-    if debug_caper:
-        cmd += ['--debug']
-    print(' '.join(cmd))
-
-    cli_main(cmd)
-    m_dict = json.loads(metadata.read_text())
-
-    assert m_dict['status'] == 'Succeeded'
-
-    # test CromwellMetadata.gcp_monitor() here
-    # since it's for gcp only and this function is one of the two
-    # test functions ran on a gcp backend.
-    # task main.t1 has sleep 10 so that monitoring_script has time to
-    # write monitoring data to `monitoringLog` file
-    cm = CromwellMetadata(m_dict)
-    monitor_data = cm.gcp_monitor()
-    for data in monitor_data:
-        instance_cpu = data['instance']['cpu']
-        instance_mem = data['instance']['mem']
-        instance_disk = data['instance']['disk']
-        assert instance_cpu >= 1
-        assert instance_mem >= 1024 * 1024 * 1024
-        assert instance_disk >= 10 * 1024 * 1024 * 1024
-
-        max_cpu_percent = data['stats']['max']['cpu_pct']
-        max_mem = data['stats']['max']['mem']
-        max_disk = data['stats']['max']['disk']
-        if max_cpu_percent or data['task_name'] == 'main.t1':
-            assert max_cpu_percent <= 100.0
-        if max_mem or data['task_name'] == 'main.t1':
-            assert max_mem <= instance_mem
-        if max_disk or data['task_name'] == 'main.t1':
-            assert max_disk <= instance_disk
-
-    # test cleanup on gcp backend (gs://)
-    root_out_dir = cm.data['workflowRoot']
-
-    # remote metadata JSON file on workflow's root output dir.
-    remote_metadata_json_file = os.path.join(root_out_dir, 'metadata.json')
-    assert GCSURI(remote_metadata_json_file).exists
-
-    # dry-run should not delete anything
-    cm.cleanup(dry_run=True)
-    assert GCSURI(remote_metadata_json_file).exists
-
-    cm.cleanup(dry_run=False)
-    assert not GCSURI(remote_metadata_json_file).exists
diff --git a/tests/test_cli_server_client_gcp.py b/tests/test_cli_server_client_gcp.py
deleted file mode 100644
index c2b42e5..0000000
--- a/tests/test_cli_server_client_gcp.py
+++ /dev/null
@@ -1,143 +0,0 @@
-"""This does not cover all CLI parameters defined in caper/caper_args.py.
-gcp (Google Cloud Platform) backend is tested here with server/client functions.
-"""
-import os
-import time
-
-import pytest
-from autouri import AutoURI
-
-from caper.cli import main as cli_main
-from caper.cromwell_rest_api import CromwellRestAPI
-from caper.wdl_parser import WDLParser
-
-from .example_wdl import make_directory_with_wdls
-
-TIMEOUT_SERVER_SPIN_UP = 500
-TIMEOUT_SERVER_RUN_WORKFLOW = 960
-
-
-@pytest.mark.google_cloud
-@pytest.mark.integration
-def test_server_client(
-    tmp_path,
-    gcs_root,
-    ci_prefix,
-    cromwell,
-    womtool,
-    gcp_prj,
-    gcp_service_account_key_json,
-    debug_caper,
-):
-    """Test server, client stuffs"""
-    # server command line
-    server_port = 8015
-
-    out_gcs_bucket = os.path.join(gcs_root, 'caper_out', ci_prefix)
-    tmp_gcs_bucket = os.path.join(gcs_root, 'caper_tmp')
-
-    cmd = ['server']
-    cmd += ['--local-loc-dir', str(tmp_path / 'tmp_dir')]
-    cmd += ['--backend', 'gcp']
-    if gcp_service_account_key_json:
-        cmd += ['--gcp-service-account-key-json', gcp_service_account_key_json]
-    cmd += ['--gcp-prj', gcp_prj]
-    cmd += ['--gcp-zones', 'us-west1-a,us-west1-b']
-    cmd += ['--gcp-out-dir', out_gcs_bucket]
-    cmd += ['--gcp-loc-dir', tmp_gcs_bucket]
-    cmd += ['--cromwell-stdout', str(tmp_path / 'cromwell_stdout.o')]
-    cmd += ['--db', 'in-memory']
-    cmd += ['--db-timeout', '500000']
-    cmd += ['--file-db', str(tmp_path / 'file_db_prefix')]
-    cmd += ['--max-concurrent-tasks', '2']
-    cmd += ['--max-concurrent-workflows', '2']
-    cmd += ['--disable-call-caching']
-    cmd += ['--local-hash-strat', 'path']
-    cmd += ['--local-out-dir', str(tmp_path / 'out_dir')]
-    cmd += ['--cromwell', cromwell]
-    cmd += ['--java-heap-server', '8G']
-    cmd += ['--port', str(server_port)]
-    if debug_caper:
-        cmd += ['--debug']
-    print(' '.join(cmd))
-
-    try:
-        th = cli_main(cmd, nonblocking_server=True)
-
-        # wait until server is ready to take submissions
-        t_start = time.time()
-        while th.status is None:
-            time.sleep(1)
-            if time.time() - t_start > TIMEOUT_SERVER_SPIN_UP:
-                raise TimeoutError('Timed out waiting for Cromwell server spin-up.')
-
-        # prepare WDLs and input JSON, imports to be submitted
-        make_directory_with_wdls(str(tmp_path))
-        wdl = tmp_path / 'main.wdl'
-        inputs = tmp_path / 'inputs.json'
-        p = WDLParser(str(wdl))
-        imports = p.zip_subworkflows(str(tmp_path / 'imports.zip'))
-
-        # test "submit" with on_hold
-        cmd = ['submit', str(wdl)]
-        if gcp_service_account_key_json:
-            cmd += ['--gcp-service-account-key-json', gcp_service_account_key_json]
-        cmd += ['--port', str(server_port)]
-        cmd += ['--inputs', str(inputs)]
-        cmd += ['--imports', str(imports)]
-        cmd += ['--gcp-zones', 'us-west1-a,us-west1-b']
-        cmd += ['--gcp-loc-dir', tmp_gcs_bucket]
-        cmd += ['--ignore-womtool']
-        cmd += ['--java-heap-womtool', '2G']
-        cmd += ['--max-retries', '1']
-        cmd += ['--docker', 'ubuntu:latest']
-        cmd += ['--backend', 'gcp']
-        cmd += ['--hold']
-        if debug_caper:
-            cmd += ['--debug']
-        cli_main(cmd)
-
-        time.sleep(10)
-
-        # find workflow ID
-        cra = CromwellRestAPI(hostname='localhost', port=server_port)
-        workflow_id = cra.find(['*'])[0]['id']
-
-        m = cra.get_metadata([workflow_id])[0]
-        assert m['status'] == 'On Hold'
-
-        # unhold it
-        cmd = ['unhold', workflow_id]
-        cmd += ['--port', str(server_port)]
-        cli_main(cmd)
-
-        time.sleep(5)
-
-        m = cra.get_metadata([workflow_id])[0]
-        assert m['status'] in ('Submitted', 'Running')
-
-        t_start = time.time()
-        while True:
-            time.sleep(5)
-            m = cra.get_metadata([workflow_id])[0]
-            workflow_root = m.get('workflowRoot')
-            if workflow_root:
-                metadata_json_file = os.path.join(workflow_root, 'metadata.json')
-            else:
-                metadata_json_file = None
-            print('polling: ', workflow_id, m['status'], metadata_json_file)
-
-            if m['status'] in ('Failed', 'Succeeded'):
-                if AutoURI(metadata_json_file).exists:
-                    break
-            elif metadata_json_file:
-                assert not AutoURI(metadata_json_file).exists
-
-            if time.time() - t_start > TIMEOUT_SERVER_RUN_WORKFLOW:
-                raise TimeoutError('Timed out waiting for workflow being done.')
-
-    finally:
-        # all done. so stop the server
-        if th:
-            th.stop()
-            th.join()
diff --git a/tests/test_nb_subproc_thread.py b/tests/test_nb_subproc_thread.py
deleted file mode 100644
index 412a3d0..0000000
--- a/tests/test_nb_subproc_thread.py
+++ /dev/null
@@ -1,117 +0,0 @@
-import os
-import time
-
-import pytest
-
-from caper.nb_subproc_thread import NBSubprocThread
-
-SH_CONTENTS = """#!/bin/bash
-
-echoerr() { echo "$@" 1>&2; }
-
-NUM=$1
-if [ -z "$NUM" ]
-then
-  NUM=10
-fi
-
-echo $NUM
-
-# NUM kitties (1 kitty per sec)
-for i in $(seq 1 $NUM)
-do
-  echo "hello kitty $i-1. (STDOUT)"
-  sleep 0.25
-  echoerr "hello kitty $i-1. (STDERR)"
-  sleep 0.25
-  echoerr "hello kitty $i-2. (STDERR)"
-  sleep 0.25
-  echo "hello kitty $i-2. (STDOUT)"
-  sleep 0.25
-done
-
-exit 10
-"""
-
-
-def on_stdout(stdout):
-    print('captured stdout:', stdout)
-    assert stdout.endswith('\n')
-
-
-def on_stderr(stderr):
-    print('captured stderr:', stderr)
-    assert stderr.endswith('\n')
-
-
-def on_poll():
-    print('polling')
-
-
-def on_finish():
-    return 'done'
-
-
-def test_nb_subproc_thread(tmp_path):
-    sh = tmp_path / 'test.sh'
-    sh.write_text(SH_CONTENTS)
-
-    th = NBSubprocThread(
-        args=['bash', str(sh)],
-        on_poll=on_poll,
-        on_stdout=on_stdout,
-        on_stderr=on_stderr,
-        on_finish=on_finish,
-        poll_interval=0.1,
-    )
-    assert th.returnvalue is None
-    assert not th.is_alive()
-    th.start()
-    assert th.is_alive()
-    # rc is None while running
-    assert th.returncode is None
-    th.join()
-    assert th.returncode == 10
-    assert th.returnvalue == 'done'
-
-
-def test_nb_subproc_thread_stopped(tmp_path):
-    sh = tmp_path / 'test.sh'
-    sh.write_text(SH_CONTENTS)
-
-    th = NBSubprocThread(args=['bash', str(sh)], on_stdout=on_stdout)
-    th.start()
-    time.sleep(2)
-    assert th.is_alive()
-    th.stop(wait=True)
-    assert not th.is_alive()
-    # rc should be is None if terminated
-    assert th.returncode is not None
-    # subprocess is terminated until it reaches kitty 4 (4 sec > 2 sec).
-    assert 'hello kitty 4' not in th.stderr
-
-
-def test_nb_subproc_thread_nonzero_rc():
-    for rc in range(10):
-        th = NBSubprocThread(
-            args=['bash', '-c', 'exit {rc}'.format(rc=rc)], on_stderr=on_stderr
-        )
-        th.start()
-        th.join()
-        assert th.returncode == rc
-
-
-@pytest.mark.parametrize('test_app,expected_rc', [('cat', 1), ('ls', 2), ('java', 1)])
-def test_nb_subproc_thread_nonzero_rc_for_real_apps(test_app, expected_rc):
-    test_str = 'asdfasf-10190212-zxcv'
-    if os.path.exists(test_str):
-        raise ValueError('Test string should not be an existing file.')
-
-    th = NBSubprocThread(
-        args=[test_app, test_str], on_stdout=on_stdout, on_stderr=on_stderr
-    )
-    th.start()
-    th.join()
-    assert th.returncode == expected_rc
-    assert test_str in th.stderr
-    assert th.stdout == ''
diff --git a/tests/test_resource_analysis.py b/tests/test_resource_analysis.py
deleted file mode 100644
index 44ffa47..0000000
--- a/tests/test_resource_analysis.py
+++ /dev/null
@@ -1,86 +0,0 @@
-"""Test is based on a metadata JSON file generated from
-running atac-seq-pipeline v1.8.0 with the following input JSON.
-gs://encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ_subsampled_caper.json
-"""
-
-import pytest
-
-from caper.resource_analysis import LinearResourceAnalysis, ResourceAnalysis
-
-
-def test_resource_analysis_abstract_class(gcp_res_analysis_metadata):
-    with pytest.raises(TypeError):
-        # abstract base-class
-        ResourceAnalysis()
-
-
-def test_resource_analysis_analyze_task(gcp_res_analysis_metadata):
-    analysis = LinearResourceAnalysis()
-    analysis.collect_resource_data([gcp_res_analysis_metadata])
-
-    result_align1 = analysis.analyze_task(
-        'atac.align',
-        in_file_vars=['fastqs_R1'],
-        reduce_in_file_vars=None,
-        target_resources=['stats.max.mem', 'stats.mean.cpu_pct'],
-    )
-    assert result_align1['x'] == {'fastqs_R1': [15643136, 18963919]}
-    assert 'stats.mean.cpu_pct' in result_align1['y']
-    assert 'stats.max.mem' in result_align1['y']
-    assert 'stats.max.disk' not in result_align1['y']
-    assert list(result_align1['y'].keys()) == list(result_align1['coeffs'].keys())
-    assert result_align1['coeffs']['stats.mean.cpu_pct'][0][0] == pytest.approx(
-        1.6844513715565233e-06
-    )
-    assert result_align1['coeffs']['stats.mean.cpu_pct'][1] == pytest.approx(
-        42.28561239506905
-    )
-    assert result_align1['coeffs']['stats.max.mem'][0][0] == pytest.approx(
-        48.91222341236991
-    )
-    assert result_align1['coeffs']['stats.max.mem'][1] == pytest.approx(
-        124314029.09791338
-    )
-
-    result_align2 = analysis.analyze_task(
-        'atac.align', in_file_vars=['fastqs_R2'], reduce_in_file_vars=sum
-    )
-    assert result_align2['x'] == {'sum(fastqs_R2)': [16495088, 20184668]}
-    assert 'stats.mean.cpu_pct' not in result_align2['y']
-    assert 'stats.max.mem' in result_align2['y']
-    assert 'stats.max.disk' in result_align2['y']
-    assert list(result_align2['y'].keys()) == list(result_align2['coeffs'].keys())
-
-    result_align_star = analysis.analyze_task('atac.align*', reduce_in_file_vars=max)
-    assert result_align_star['x'] == {
-        'max(chrsz,fastqs_R1,fastqs_R2,idx_tar,tmp_fastqs)': [
-            32138224,
-            39148587,
-            3749246230,
-            3749246230,
-        ]
-    }
-
-
-def test_resource_analysis_analyze(gcp_res_analysis_metadata):
-    """Test method analyze() which analyze all tasks defined in in_file_vars."""
-    analysis = LinearResourceAnalysis()
-    analysis.collect_resource_data([gcp_res_analysis_metadata])
-
-    result = analysis.analyze(
-        in_file_vars={
-            'atac.align*': ['fastqs_R1', 'fastqs_R2'],
-            'atac.filter*': ['bam'],
-        }
-    )
-    assert len(result) == 2
-    assert result['atac.align*']['x'] == {
-        'sum(fastqs_R1,fastqs_R2)': [32138224, 39148587, 32138224, 39148587]
-    }
-    assert result['atac.filter*']['x'] == {
-        'sum(bam)': [61315022, 76789196, 61315022, 76789196]
-    }
-
-    result_all = analysis.analyze()
-    # 38 tasks in total
-    assert len(result_all) == 38