diff --git a/README.md b/README.md
index 1d8afe2..c02fadc 100644
--- a/README.md
+++ b/README.md
@@ -73,6 +73,10 @@ To access other endpoints, export the environment variable `BEAGLE_ENDPOINT`.
   ```
   beaglecli run latest-info --request-id requests.txt --completed --output-metadata-only --max-pages
   ```
+- Return and clean output metadata for a given request id from files api
+  ```
+  beaglecli files list --metadata=igoRequestId:13167_C  --file-type fastq --all --packaged
+  ```
 Note: Use `requests.txt` as a template for providing a multiple request ids
 
 #### Troubleshooting
diff --git a/apps/access/__init__.py b/apps/access/__init__.py
index 32c492d..59262f0 100644
--- a/apps/access/__init__.py
+++ b/apps/access/__init__.py
@@ -18,33 +18,33 @@
 def access_commands(arguments, config):
     print('Running ACCESS')
 
-    request_id, sample_id, apps = get_arguments(arguments)
+    request_id, sample_id, apps, show_all_runs = get_arguments(arguments)
     tags = '{"cmoSampleIds":"%s"}' % sample_id if sample_id else '{"igoRequestId":"%s"}' % request_id
     if arguments.get('link'):
         for (app, app_version) in apps:
             (app_name, directory) = FLAG_TO_APPS[app]
-            operator_run = get_operator_run(app_name, app_version, tags, config)
+            operator_run = get_operator_run(app_name, app_version, tags, config, show_all_runs)
             if operator_run:
                 if arguments.get('--single-dir'):
                     if app == "bams":
-                        link_bams_to_single_dir(operator_run, app, request_id, sample_id, arguments, config)
+                        link_bams_to_single_dir(operator_run, app, request_id, sample_id, arguments, config, show_all_runs)
                     else:
                         print("Apps other than bams not supported at this time")
                 else:
-                    link_app(operator_run, directory, request_id, sample_id, arguments, config)
+                    link_app(operator_run, directory, request_id, sample_id, arguments, config, show_all_runs)
 
     if arguments.get('link-patient'):
         for (app, app_version) in apps:
             (app_name, directory) = FLAG_TO_APPS[app]
-            operator_run = get_operator_run(app_name, app_version, tags, config)
+            operator_run = get_operator_run(app_name, app_version, tags, config, show_all_runs)
             if operator_run:
                 if(app == "bams"):
-                    link_bams_by_patient_id(operator_run, "bams", request_id, sample_id, arguments, config)
+                    link_bams_by_patient_id(operator_run, "bams", request_id, sample_id, arguments, config, show_all_runs)
                 else:
                     link_single_sample_workflows_by_patient_id(operator_run, directory, request_id, sample_id, arguments,
-                                                           config)
+                                                           config, show_all_runs)
 
-def get_operator_run(app_name, app_version=None, tags=None, config=None):
+def get_operator_run(app_name, app_version=None, tags=None, config=None, show_all_runs=False):
     latest_operator_run = {
         "tags": tags,
         "status": "COMPLETED",
@@ -52,6 +52,9 @@ def get_operator_run(app_name, app_version=None, tags=None, config=None):
         "app_name": app_name
     }
 
+    if show_all_runs:
+        latest_operator_run.pop("status")
+
     if app_version:
         latest_operator_run["app_version"] = app_version
 
@@ -75,6 +78,7 @@ def get_arguments(arguments):
     request_id = arguments.get('--request-id')
     sample_id = arguments.get('--sample-id')
     app_tags = arguments.get('--apps')
+    show_all_runs = arguments.get('--all-runs') or False
     if request_id:
         request_id = request_id[0]
 
@@ -86,16 +90,19 @@ def get_arguments(arguments):
         else:
             apps.append((r[0], None))
 
-    return request_id, sample_id, apps
+    return request_id, sample_id, apps, show_all_runs
 
 
-def get_runs(operator_run_id, config):
+def get_runs(operator_run_id, config, show_all_runs):
     run_params = {
         "operator_run": operator_run_id,
         "page_size": 1000,
         "status": "COMPLETED"
     }
 
+    if show_all_runs:
+        run_params.pop("status")
+
     response = requests.get(urljoin(config['beagle_endpoint'], config['api']['run']),
                             headers={'Authorization': 'Bearer %s' % config['token']}, params=run_params)
 
@@ -117,7 +124,7 @@ def get_files_by_run_id(run_id, config):
 def get_file_path(file):
     return file["location"][7:]
 
-def link_app(operator_run, directory, request_id, sample_id, arguments, config):
+def link_app(operator_run, directory, request_id, sample_id, arguments, config, show_all_runs):
     version = arguments.get("--dir-version") or operator_run["app_version"]
     should_delete = arguments.get("--delete") or False
 
@@ -126,7 +133,7 @@ def link_app(operator_run, directory, request_id, sample_id, arguments, config):
     path = path_without_version / version
     path.mkdir(parents=True, exist_ok=True, mode=0o755)
 
-    runs = get_runs(operator_run["id"], config)
+    runs = get_runs(operator_run["id"], config, show_all_runs)
     if not runs:
         return
 
@@ -156,13 +163,13 @@ def link_app(operator_run, directory, request_id, sample_id, arguments, config):
     return "Completed"
 
 
-def link_single_sample_workflows_by_patient_id(operator_run, directory, request_id, sample_id, arguments, config):
+def link_single_sample_workflows_by_patient_id(operator_run, directory, request_id, sample_id, arguments, config, show_all_runs):
     version = arguments.get("--dir-version") or operator_run["app_version"]
     should_delete = arguments.get("--delete") or False
 
     path = Path("./") / directory
 
-    runs = get_runs(operator_run["id"], config)
+    runs = get_runs(operator_run["id"], config, show_all_runs)
     if not runs:
         return
 
@@ -199,12 +206,12 @@ def link_single_sample_workflows_by_patient_id(operator_run, directory, request_
 
     return "Completed"
 
-def link_bams_to_single_dir(operator_run, directory, request_id, sample_id, arguments, config):
+def link_bams_to_single_dir(operator_run, directory, request_id, sample_id, arguments, config, show_all_runs):
     version = arguments.get("--dir-version") or operator_run["app_version"]
 
     path = Path("./") / directory / ("Project_" + request_id)
 
-    runs = get_runs(operator_run["id"], config)
+    runs = get_runs(operator_run["id"], config, show_all_runs)
 
     if not runs:
         return
@@ -253,13 +260,13 @@ def link_bams_to_single_dir(operator_run, directory, request_id, sample_id, argu
 
     return "Completed"
 
-def link_bams_by_patient_id(operator_run, directory, request_id, sample_id, arguments, config):
+def link_bams_by_patient_id(operator_run, directory, request_id, sample_id, arguments, config, show_all_runs):
     version = arguments.get("--dir-version") or operator_run["app_version"]
     should_delete = arguments.get("--delete") or False
 
     path = Path("./") / directory
 
-    runs = get_runs(operator_run["id"], config)
+    runs = get_runs(operator_run["id"], config, show_all_runs)
 
     if not runs:
         return
diff --git a/apps/cleaning/__init__.py b/apps/cleaning/__init__.py
new file mode 100644
index 0000000..ce836c3
--- /dev/null
+++ b/apps/cleaning/__init__.py
@@ -0,0 +1,82 @@
+import json
+import pandas as pd 
+from collections import defaultdict
+from urllib.parse import urljoin
+from pathlib import Path
+
+C_NAMES = [
+    "igoRequestId",
+    "cmoSampleName",
+    "sampleName",
+    "sampleClass",
+    "cmoPatientId",
+    "investigatorSampleId",
+    "oncotreeCode",
+    "tumorOrNormal",
+    "tissueLocation",
+    "sampleOrigin",
+    "preservation",
+    "collectionYear",
+    "sex",
+    "species",
+    "tubeId",
+    "cfDNA2dBarcode",
+    "baitSet",
+    "qcReports",
+    "barcodeId",
+    "barcodeIndex",
+    "libraryIgoId",
+    "libraryVolume",
+    "libraryConcentrationNgul",
+    "dnaInputNg",
+    "captureConcentrationNm",
+    "captureInputNg",
+    "captureName"
+]
+
+
+def _clean_json(data):
+    # Iterating through the json
+    # list
+    # should do other check for format changes 
+    results = [] 
+    for i in range(0,len(data["results"])):
+        results.append(data['results'][i]['metadata']) 
+    df = pd.DataFrame(results)
+    # check all columns are present
+    if not set(C_NAMES).issubset(df.columns): 
+        ValueError('missing column names expected in file metadata. Format has changed, or JSON is badly formed.')
+    # subset to important columns
+    df = df[C_NAMES]
+    # normalize columns 
+    bf_list = [i for i in df.columns if isinstance(df[i][0],list)]
+    cleaned_columns = [df[column].apply(lambda x: x[0] if isinstance(x, list) else x) for column in bf_list]
+    df[bf_list] = pd.concat(cleaned_columns, axis=1)
+    bf_dict = [i for i in df.columns if isinstance(df[i][0],dict)]
+    normalized_columns = [pd.json_normalize(df[column]) for column in bf_dict]
+    normalized_df = pd.concat(normalized_columns, axis=1)
+    df = df.drop(columns=bf_dict)
+    df = pd.concat([df, normalized_df], axis=1)
+    df = df.drop_duplicates()
+    return df
+
+def _write_output(data, out_data):
+    # csv
+    out_name = data['results'][0]['metadata']['igoRequestId']
+    out_data = out_data.loc[:,~out_data.columns.duplicated()].copy()
+    out_data.to_csv('{out_name}.csv'.format(out_name=out_name), index=False)
+    # json 
+    out_data = out_data.to_dict('records')
+    with open('{out_name}.json'.format(out_name=out_name), 'w') as fout:
+        json.dump(out_data , fout, indent=4)
+
+
+
+def clean_json_comands(results):
+    # get args
+    datain=json.loads(results)
+    # clean json
+    dataout = _clean_json(datain)
+    # write out 
+    _write_output(datain, dataout)
+    
\ No newline at end of file
diff --git a/apps/cmoch/__init__.py b/apps/cmoch/__init__.py
index d94693a..a872030 100644
--- a/apps/cmoch/__init__.py
+++ b/apps/cmoch/__init__.py
@@ -7,46 +7,46 @@
 import requests
 
 FLAG_TO_APPS = {
-    "bams": ("Access CMO-CH", "bams"),
+    "bams": ("cmo-ch nucleo", "bams"),
 }
 
 
 def cmoch_commands(arguments, config):
     print('Running CMOCH')
 
-    request_id, sample_id, apps = get_arguments(arguments)
+    request_id, sample_id, apps, show_all_runs = get_arguments(arguments)
     tags = '{"cmoSampleId":"%s"}' % sample_id if sample_id else '{"igoRequestId":"%s"}' % request_id
     if arguments.get('link'):
         for (app, app_version) in apps:
             (app_name, directory) = FLAG_TO_APPS[app]
             operator_run = get_operator_run(
-                app_name, app_version, tags, config)
+                app_name, app_version, tags, config, show_all_runs)
             if operator_run:
                 if arguments.get('--single-dir'):
                     if app == "bams":
                         link_bams_to_single_dir(
-                            operator_run, app, request_id, sample_id, arguments, config)
+                            operator_run, app, request_id, sample_id, arguments, config, show_all_runs)
                     else:
                         print("Apps other than bams not supported at this time")
                 else:
                     link_app(operator_run, directory, request_id,
-                             sample_id, arguments, config)
+                             sample_id, arguments, config, show_all_runs)
 
     if arguments.get('link-patient'):
         for (app, app_version) in apps:
             (app_name, directory) = FLAG_TO_APPS[app]
             operator_run = get_operator_run(
-                app_name, app_version, tags, config)
+                app_name, app_version, tags, config, show_all_runs)
             if operator_run:
                 if(app == "bams"):
                     link_bams_by_patient_id(
-                        operator_run, "bams", request_id, sample_id, arguments, config)
+                        operator_run, "bams", request_id, sample_id, arguments, config, show_all_runs)
                 else:
                     link_single_sample_workflows_by_patient_id(operator_run, directory, request_id, sample_id, arguments,
-                                                               config)
+                                                               config, show_all_runs)
 
 
-def get_operator_run(app_name, app_version=None, tags=None, config=None):
+def get_operator_run(app_name, app_version=None, tags=None, config=None, show_all_runs=False):
     latest_operator_run = {
         "tags": tags,
         "status": "COMPLETED",
@@ -54,6 +54,9 @@ def get_operator_run(app_name, app_version=None, tags=None, config=None):
         "app_name": app_name
     }
 
+    if show_all_runs:
+        latest_operator_run.pop("status")
+
     if app_version:
         latest_operator_run["app_version"] = app_version
 
@@ -75,6 +78,7 @@ def get_arguments(arguments):
     request_id = arguments.get('--request-id')
     sample_id = arguments.get('--sample-id')
     app_tags = arguments.get('--apps')
+    show_all_runs = arguments.get('--all-runs') or False
     if request_id:
         request_id = request_id[0]
 
@@ -86,16 +90,19 @@ def get_arguments(arguments):
         else:
             apps.append((r[0], None))
 
-    return request_id, sample_id, apps
+    return request_id, sample_id, apps, show_all_runs
 
 
-def get_runs(operator_run_id, config):
+def get_runs(operator_run_id, config, show_all_runs):
     run_params = {
         "operator_run": operator_run_id,
         "page_size": 1000,
         "status": "COMPLETED"
     }
 
+    if show_all_runs:
+        run_params.pop("status")
+
     response = requests.get(urljoin(config['beagle_endpoint'], config['api']['run']),
                             headers={'Authorization': 'Bearer %s' % config['token']}, params=run_params)
 
@@ -120,7 +127,7 @@ def get_file_path(file):
     return file["location"][7:]
 
 
-def link_app(operator_run, directory, request_id, sample_id, arguments, config):
+def link_app(operator_run, directory, request_id, sample_id, arguments, config, show_all_runs):
     version = arguments.get("--dir-version") or operator_run["app_version"]
     should_delete = arguments.get("--delete") or False
 
@@ -129,7 +136,7 @@ def link_app(operator_run, directory, request_id, sample_id, arguments, config):
     path = path_without_version / version
     path.mkdir(parents=True, exist_ok=True, mode=0o755)
 
-    runs = get_runs(operator_run["id"], config)
+    runs = get_runs(operator_run["id"], config, show_all_runs)
     if not runs:
         return
 
@@ -161,13 +168,13 @@ def link_app(operator_run, directory, request_id, sample_id, arguments, config):
     return "Completed"
 
 
-def link_single_sample_workflows_by_patient_id(operator_run, directory, request_id, sample_id, arguments, config):
+def link_single_sample_workflows_by_patient_id(operator_run, directory, request_id, sample_id, arguments, config, show_all_runs):
     version = arguments.get("--dir-version") or operator_run["app_version"]
     should_delete = arguments.get("--delete") or False
 
     path = Path("./") / directory
 
-    runs = get_runs(operator_run["id"], config)
+    runs = get_runs(operator_run["id"], config, show_all_runs)
     if not runs:
         return
 
@@ -208,12 +215,12 @@ def link_single_sample_workflows_by_patient_id(operator_run, directory, request_
     return "Completed"
 
 
-def link_bams_to_single_dir(operator_run, directory, request_id, sample_id, arguments, config):
+def link_bams_to_single_dir(operator_run, directory, request_id, sample_id, arguments, config, show_all_runs):
     version = arguments.get("--dir-version") or operator_run["app_version"]
 
     path = Path("./") / directory / ("Project_" + request_id)
 
-    runs = get_runs(operator_run["id"], config)
+    runs = get_runs(operator_run["id"], config, show_all_runs)
 
     if not runs:
         return
@@ -264,13 +271,13 @@ def link_bams_to_single_dir(operator_run, directory, request_id, sample_id, argu
     return "Completed"
 
 
-def link_bams_by_patient_id(operator_run, directory, request_id, sample_id, arguments, config):
+def link_bams_by_patient_id(operator_run, directory, request_id, sample_id, arguments, config, show_all_runs):
     version = arguments.get("--dir-version") or operator_run["app_version"]
     should_delete = arguments.get("--delete") or False
 
     path = Path("./") / directory
 
-    runs = get_runs(operator_run["id"], config)
+    runs = get_runs(operator_run["id"], config, show_all_runs)
 
     if not runs:
         return
diff --git a/beaglecli b/beaglecli
index c37b282..76510cd 100755
--- a/beaglecli
+++ b/beaglecli
@@ -31,6 +31,7 @@ import csv
 from apps.access import access_commands
 from apps.cmoch import cmoch_commands
 from apps.lims import lims_commands
+from apps.cleaning import clean_json_comands
 
 
 BEAGLE_ENDPOINT = os.environ.get('BEAGLE_ENDPOINT', 'http://voyager:5001')
@@ -42,7 +43,7 @@ CONFIG_TEMPLATE = {
     'token': '',
     'refresh': '',
     'next': None,
-    'prev': None,
+    'prev': None
 }
 
 
@@ -72,7 +73,7 @@ Usage:
   beaglecli files create <file_path> <file_type> <file_group_id> [--metadata-path=<metadata_path>] [--size=<size>]
   beaglecli files update <file_id> [--file-path=<file_path>] [--file-type=<file_type>] [--file-group=<file_group_id>] [--metadata-path=<metadata_path>] [--size=<size>]
   beaglecli files patch <file_id> [--file-path=<file_path>] [--file-type=<file_type>] [--file-group=<file_group_id>] [--metadata=<metadata>]... [--size=<size>]
-  beaglecli files list [--page-size=<page_size>] [--path=<path>]... [--metadata=<metadata>]... [--file-group=<file_group>]... [--file-name=<file_name>]... [--filename-regex=<filename_regex>] [--file-type=<file_type>]...
+  beaglecli files list [--page-size=<page_size>] [--path=<path>]... [--metadata=<metadata>]... [--file-group=<file_group>]... [--file-name=<file_name>]... [--filename-regex=<filename_regex>] [--file-type=<file_type>]... [--all]... [--packaged]...
   beaglecli files delete --file-id=<file_id>...
   beaglecli sample create <sample-id>
   beaglecli sample list [--sample-id=<sample-id>]
@@ -84,8 +85,8 @@ Usage:
   beaglecli file-group create <file_group_name> <storage>
   beaglecli file-group list [--page-size=<page_size>]
   beaglecli etl delete --job-id=<job_id>...
-  beaglecli run list [--page-size=<page_size>] [--request-id=<request_id>]... [--tags=<tags>]... [--apps="apps"]... [--job-groups=<job_groups>]... [--jira-ids=<jira_ids>]...
-  beaglecli run latest-info [--request-id=<request_id | request_ids.csv> ] [--job-group=<job_group>] [--apps="apps"]... [--jira-id=<jira_id>] [--output-file=<output_file>] [--completed][--page-size=<page_size>] [--output-metadata-only] [--max-pages]
+  beaglecli run list [--page-size=<page_size>] [--request-id=<request_id>]... [--tags=<tags>]... [--apps="apps"]... [--job-groups=<job_groups>]... [--jira-ids=<jira_ids>]... [--all]...
+  beaglecli run latest-info [--request-id=<request_id | request_ids.csv> ] [--job-group=<job_group>] [--apps="apps"]... [--jira-id=<jira_id>] [--output-file=<output_file>] [--completed][--page-size=<page_size>] [--output-metadata-only] [--max-pages] [--all]...
   beaglecli run get <run_id>
   beaglecli run submit-request --pipeline=<pipeline> [--request-ids=<request_ids>] [--job-group-id=<job_group_id>] [--for-each=<True or False>]
   beaglecli run submit-runs --pipelines=<pipeline>... --versions=<versions>...[--run-file=<run_file>] [--run-ids=<run_ids>]... [--job-group-id=<job_group_id>] [--for-each=<True or False>]
@@ -93,10 +94,10 @@ Usage:
   beaglecli tempo-mpgen
   beaglecli tempo-mpgen override --normals=<normal_samples> --tumors=<tumor_samples>
   beaglecli lims metadata [--request-id=<request_id>]
-  beaglecli access link [--single-dir] [--request-id=<request_id>] [--sample-id=<sample_id>] [--dir-version=<dir_version>] [--apps=<msi|cnv|sv|snv|bams|nucleo>]... [--delete]
-  beaglecli access link-patient [--request-id=<request_id>] [--sample-id=<sample_id>] [--dir-version=<dir_version>] [--apps=<msi|cnv|sv|snv|bams|nucleo>]... [--delete]
-  beaglecli cmoch link [--single-dir] [--request-id=<request_id>] [--sample-id=<sample_id>] [--dir-version=<dir_version>] [--apps=<bams>]... [--delete]
-  beaglecli cmoch link-patient [--request-id=<request_id>] [--sample-id=<sample_id>] [--dir-version=<dir_version>] [--apps=<bams>]... [--delete]
+  beaglecli access link [--single-dir] [--all-runs] [--request-id=<request_id>] [--sample-id=<sample_id>] [--dir-version=<dir_version>] [--apps=<msi|cnv|sv|snv|bams|nucleo>]... [--delete]
+  beaglecli access link-patient [--all-runs] [--request-id=<request_id>] [--sample-id=<sample_id>] [--dir-version=<dir_version>] [--apps=<msi|cnv|sv|snv|bams|nucleo>]... [--delete]
+  beaglecli cmoch link [--single-dir] [--all-runs] [--request-id=<request_id>] [--sample-id=<sample_id>] [--dir-version=<dir_version>] [--apps=<bams>]... [--delete]
+  beaglecli cmoch link-patient [--all-runs] [--request-id=<request_id>] [--sample-id=<sample_id>] [--dir-version=<dir_version>] [--apps=<bams>]... [--delete]
   beaglecli --version
 
 Options:
@@ -584,6 +585,8 @@ def _list_files(arguments, config):
     filename_regex = arguments.get('--filename-regex')
     page_size = arguments.get('--page-size')
     file_type = arguments.get('--file-type')
+    all_pages = arguments.get('--all')
+    packaged = arguments.get('--packaged')
     params = dict()
     params['path'] = paths
     params['metadata'] = metadata
@@ -591,11 +594,15 @@ def _list_files(arguments, config):
     params['file_name'] = file_name
     params['filename_regex'] = filename_regex
     params['file_type'] = file_type
-    if page_size:
-        params['page_size'] = page_size
+    if all_pages:
+        count_params = params 
+        count_params['count'] = True 
+        params['page_size'] = requests.get(urljoin(BEAGLE_ENDPOINT, API['files']), headers={'Authorization': 'Bearer %s' % config.token}, params=count_params).json()['count']
     response = requests.get(urljoin(BEAGLE_ENDPOINT, API['files']), headers={
                             'Authorization': 'Bearer %s' % config.token}, params=params)
     response_json = json.dumps(response.json(), indent=4)
+    if packaged:
+        clean_json_comands(response_json)
     _set_next_and_prev(config, response.json())
     return response_json
 
@@ -952,7 +959,6 @@ def _redact_sample(arguments, config):
     response_json = json.dumps(response.json(), indent=4)
     return response_json
 
-
 if __name__ == '__main__':
     config = Config.load()
     authenticate_command(config)
diff --git a/column_names.txt b/column_names.txt
new file mode 100644
index 0000000..a156f0a
--- /dev/null
+++ b/column_names.txt
@@ -0,0 +1,27 @@
+igoId,
+cmoSampleName,
+sampleName,
+cmoSampleClass,
+cmoPatientId,
+investigatorSampleId,
+oncoTreeCode,
+tumorOrNormal,
+tissueLocation,
+sampleOrigin,
+preservation,
+collectionYear,
+sex,
+species,
+tubeId,
+cfDNA2dBarcode,
+baitSet,
+qcReports,
+barcodeId,
+barcodeIndex,
+libraryIgoId,
+libraryVolume,
+libraryConcentrationNgul,
+dnaInputNg,
+captureConcentrationNm,
+captureInputNg,
+captureName
\ No newline at end of file
diff --git a/requirements.txt b/requirements.txt
index ac03762..6cf06d1 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,2 +1,3 @@
 docopt==0.6.2
 requests==2.22.0
+pandas
\ No newline at end of file
diff --git a/setup.py b/setup.py
index ad90de0..4ea87c0 100755
--- a/setup.py
+++ b/setup.py
@@ -6,7 +6,7 @@
 
 setuptools.setup(
     name='beaglecli',
-    version='0.3.0',
+    version='0.4.0',
     scripts=['beaglecli'] ,
     description="Beagle API command line tool",
     url="https://github.com/mskcc/beagle_cli",