Merge branch 'master' of https://github.com/arvados/bh20-seq-resource

19 files changed, 441 insertions, 184 deletions

diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py
index 9a36cae..1746587 100644
--- a/bh20seqanalyzer/main.py
+++ b/bh20seqanalyzer/main.py
@@ -20,26 +20,36 @@ def validate_upload(api, collection, validated_project,
                     fastq_project, fastq_workflow_uuid):
     col = arvados.collection.Collection(collection["uuid"])
 
+    if collection.get("status") in ("validated", "rejected"):
+        return False
+
     # validate the collection here.  Check metadata, etc.
-    valid = True
+    logging.info("Validating upload '%s' (%s)" % (collection["name"], collection["uuid"]))
 
-    if "metadata.yaml" not in col:
-        logging.warn("Upload '%s' missing metadata.yaml", collection["name"])
-        valid = False
-    else:
-        try:
-            metadata_content = ruamel.yaml.round_trip_load(col.open("metadata.yaml"))
-            metadata_content["id"] = "http://arvados.org/keep:%s/metadata.yaml" % collection["portable_data_hash"]
-            sample_id = metadata_content["sample"]["sample_id"]
-            add_lc_filename(metadata_content, metadata_content["id"])
-            valid = qc_metadata(metadata_content) and valid
-        except Exception as e:
-            logging.warn(e)
-            valid = False
-        if not valid:
-            logging.warn("Failed metadata qc")
-
-    if valid:
+    errors = []
+
+    dup = api.collections().list(filters=[["owner_uuid", "=", validated_project],
+                                          ["portable_data_hash", "=", col.portable_data_hash()]]).execute()
+    if dup["items"]:
+        # This exact collection has been uploaded before.
+        errors.append("Duplicate of %s" % ([d["uuid"] for d in dup["items"]]))
+
+    if not errors:
+        if "metadata.yaml" not in col:
+            errors.append("Missing metadata.yaml", collection["name"])
+        else:
+            try:
+                metadata_content = ruamel.yaml.round_trip_load(col.open("metadata.yaml"))
+                metadata_content["id"] = "http://arvados.org/keep:%s/metadata.yaml" % collection["portable_data_hash"]
+                sample_id = metadata_content["sample"]["sample_id"]
+                add_lc_filename(metadata_content, metadata_content["id"])
+                valid = qc_metadata(metadata_content)
+                if not valid:
+                    errors.append("Failed metadata qc")
+            except Exception as e:
+                errors.append(str(e))
+
+    if not errors:
         try:
             tgt = None
             paired = {"reads_1.fastq": "reads.fastq", "reads_1.fastq.gz": "reads.fastq.gz"}
@@ -49,36 +59,32 @@ def validate_upload(api, collection, validated_project,
                 with col.open(n, 'rb') as qf:
                     tgt = qc_fasta(qf)[0]
                     if tgt != n and tgt != paired.get(n):
-                        logging.info("Expected %s but magic says it should be %s", n, tgt)
-                        valid = False
+                        errors.append("Expected %s but magic says it should be %s", n, tgt)
                     elif tgt in ("reads.fastq", "reads.fastq.gz", "reads_1.fastq", "reads_1.fastq.gz"):
                         start_fastq_to_fasta(api, collection, fastq_project, fastq_workflow_uuid, n, sample_id)
                         return False
             if tgt is None:
-                valid = False
-                logging.warn("Upload '%s' does not contain sequence.fasta, reads.fastq or reads_1.fastq", collection["name"])
-        except ValueError as v:
-            valid = False
+                errors.append("Upload '%s' does not contain sequence.fasta, reads.fastq or reads_1.fastq", collection["name"])
+        except Exception as v:
+            errors.append(str(v))
 
-    dup = api.collections().list(filters=[["owner_uuid", "=", validated_project],
-                                          ["portable_data_hash", "=", col.portable_data_hash()]]).execute()
-    if dup["items"]:
-        # This exact collection has been uploaded before.
-        valid = False
-        logging.warn("Upload '%s' is duplicate" % collection["name"])
 
-    if valid:
+    if not errors:
         logging.info("Added '%s' to validated sequences" % collection["name"])
         # Move it to the "validated" project to be included in the next analysis
+        collection["properties"]["status"] = "validated"
         api.collections().update(uuid=collection["uuid"], body={
             "owner_uuid": validated_project,
             "name": "%s (%s)" % (collection["name"], time.asctime(time.gmtime()))}).execute()
+        return True
     else:
-        # It is invalid, delete it.
-        logging.warn("Suggest deleting '%s'" % collection["name"])
-        #api.collections().delete(uuid=collection["uuid"]).execute()
-
-    return valid
+        # It is invalid
+        logging.warn("'%s' (%s) has validation errors: %s" % (
+            collection["name"], collection["uuid"], "\n".join(errors)))
+        collection["properties"]["status"] = "rejected"
+        collection["properties"]["errors"] = errors
+        api.collections().update(uuid=collection["uuid"], body={"properties": collection["properties"]}).execute()
+        return False
 
 
 def run_workflow(api, parent_project, workflow_uuid, name, inputobj):
@@ -229,6 +235,50 @@ def upload_schema(api, workflow_def_project):
     return "keep:%s/schema.yml" % pdh
 
 
+def print_status(api, uploader_project, fmt):
+    pending = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", uploader_project]])
+    out = []
+    status = {}
+    for p in pending:
+        prop = p["properties"]
+        out.append(prop)
+        if "status" not in prop:
+            prop["status"] = "pending"
+        prop["created_at"] = p["created_at"]
+        prop["uuid"] = p["uuid"]
+        status[prop["status"]] = status.get(prop["status"], 0) + 1
+    if fmt == "html":
+        print(
+"""
+<html>
+<body>
+""")
+        print("<p>Total collections in upload project %s</p>" % len(out))
+        print("<p>Status %s</p>" % status)
+        print(
+"""
+<table>
+<tr><th>Collection</th>
+<th>Sequence label</th>
+<th>Status</th>
+<th>Errors</th></tr>
+""")
+        for r in out:
+            print("<tr valign='top'>")
+            print("<td><a href='https://workbench.lugli.arvadosapi.com/collections/%s'>%s</a></td>" % (r["uuid"], r["uuid"]))
+            print("<td>%s</td>" % r["sequence_label"])
+            print("<td>%s</td>" % r["status"])
+            print("<td><pre>%s</pre></td>" % "\n".join(r.get("errors", [])))
+            print("</tr>")
+        print(
+"""
+</table>
+</body>
+</html>
+""")
+    else:
+        print(json.dumps(out, indent=2))
+
 def main():
     parser = argparse.ArgumentParser(description='Analyze collections uploaded to a project')
     parser.add_argument('--uploader-project', type=str, default='lugli-j7d0g-n5clictpuvwk8aa', help='')
@@ -244,7 +294,9 @@ def main():
 
     parser.add_argument('--latest-result-collection', type=str, default='lugli-4zz18-z513nlpqm03hpca', help='')
     parser.add_argument('--kickoff', action="store_true")
+    parser.add_argument('--no-start-analysis', action="store_true")
     parser.add_argument('--once', action="store_true")
+    parser.add_argument('--print-status', type=str, default=None)
     args = parser.parse_args()
 
     api = arvados.api()
@@ -263,20 +315,24 @@ def main():
                                  args.exclude_list)
         return
 
+    if args.print_status:
+        print_status(api, args.uploader_project, args.print_status)
+        exit(0)
+
     logging.info("Starting up, monitoring %s for uploads" % (args.uploader_project))
 
     while True:
         move_fastq_to_fasta_results(api, args.fastq_project, args.uploader_project)
 
-        new_collections = api.collections().list(filters=[['owner_uuid', '=', args.uploader_project]]).execute()
+        new_collections = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", args.uploader_project]])
         at_least_one_new_valid_seq = False
-        for c in new_collections["items"]:
+        for c in new_collections:
             at_least_one_new_valid_seq = validate_upload(api, c,
                                                          args.validated_project,
                                                          args.fastq_project,
                                                          args.fastq_workflow_uuid) or at_least_one_new_valid_seq
 
-        if at_least_one_new_valid_seq:
+        if at_least_one_new_valid_seq and not args.no_start_analysis:
             start_pangenome_analysis(api,
                                      args.pangenome_analysis_project,
                                      args.pangenome_workflow_uuid,
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index c442af0..fd0278d 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -22,30 +22,32 @@ ARVADOS_API_HOST='lugli.arvadosapi.com'
 ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
 UPLOAD_PROJECT='lugli-j7d0g-n5clictpuvwk8aa'
 
-def qa_stuff(metadata, sequence_p1, sequence_p2):
+def qc_stuff(metadata, sequence_p1, sequence_p2, do_qc=True):
+    failed = False
     try:
-        log.debug("Checking metadata")
-        if not qc_metadata(metadata.name):
+        log.debug("Checking metadata" if do_qc else "Skipping metadata check")
+        if do_qc and not qc_metadata(metadata.name):
             log.warning("Failed metadata qc")
-            exit(1)
-    except ValueError as e:
+            failed = True
+    except Exception as e:
         log.debug(e)
-        log.debug("Failed metadata qc")
         print(e)
-        exit(1)
+        failed = True
 
     target = []
     try:
-        log.debug("Checking FASTA/FASTQ QC")
-        target.append(qc_fasta(sequence_p1))
+        log.debug("FASTA/FASTQ QC" if do_qc else "Limited FASTA/FASTQ QC")
+        target.append(qc_fasta(sequence_p1, check_with_clustalw=do_qc))
         if sequence_p2:
             target.append(qc_fasta(sequence_p2))
             target[0] = ("reads_1."+target[0][0][6:], target[0][1])
             target[1] = ("reads_2."+target[1][0][6:], target[0][1])
-    except ValueError as e:
+    except Exception as e:
         log.debug(e)
-        log.debug("Failed FASTA qc")
         print(e)
+        failed = True
+
+    if failed:
         exit(1)
 
     return target
@@ -62,13 +64,14 @@ def main():
     parser = argparse.ArgumentParser(description='Upload SARS-CoV-19 sequences for analysis')
     parser.add_argument('metadata', type=argparse.FileType('r'), help='sequence metadata json')
     parser.add_argument('sequence_p1', type=argparse.FileType('rb'), help='sequence FASTA/FASTQ')
-    parser.add_argument('sequence_p2', type=argparse.FileType('rb'), default=None, help='sequence FASTQ pair')
+    parser.add_argument('sequence_p2', type=argparse.FileType('rb'), default=None, nargs='?', help='sequence FASTQ pair')
     parser.add_argument("--validate", action="store_true", help="Dry run, validate only")
+    parser.add_argument("--skip-qc", action="store_true", help="Skip local qc check")
     args = parser.parse_args()
 
     api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True)
 
-    target = qa_stuff(args.metadata, args.sequence_p1, args.sequence_p2)
+    target = qc_stuff(args.metadata, args.sequence_p1, args.sequence_p2, not args.skip_qc)
     seqlabel = target[0][1]
 
     if args.validate:
diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py
index e198430..37eb4e8 100644
--- a/bh20sequploader/qc_fasta.py
+++ b/bh20sequploader/qc_fasta.py
@@ -25,7 +25,7 @@ def read_fasta(sequence):
             raise ValueError("FASTA file contains multiple entries")
     return label, bases
 
-def qc_fasta(arg_sequence):
+def qc_fasta(arg_sequence, check_with_clustalw=True):
     log.debug("Starting qc_fasta")
     schema_resource = pkg_resources.resource_stream(__name__, "validation/formats")
     with tempfile.NamedTemporaryFile() as tmp:
@@ -51,47 +51,48 @@ def qc_fasta(arg_sequence):
     if seq_type == "text/fasta":
         # ensure that contains only one entry
         submitlabel, submitseq = read_fasta(sequence)
+        sequence.seek(0)
+        sequence.detach()
 
-        with tempfile.NamedTemporaryFile() as tmp1:
-            refstring = pkg_resources.resource_string(__name__, "SARS-CoV-2-reference.fasta")
-            tmp1.write(refstring)
-            tmp1.write(submitlabel.encode("utf8"))
-            tmp1.write(("".join(submitseq)).encode("utf8"))
-            tmp1.flush()
-            subbp = 0
-            refbp = 0
-            similarity = 0
-            try:
-                cmd = ["clustalw", "-infile="+tmp1.name,
-                       "-quicktree", "-iteration=none", "-type=DNA"]
-                print("QC checking similarity to reference")
-                print(" ".join(cmd))
-                result = subprocess.run(cmd, stdout=subprocess.PIPE)
-                res = result.stdout.decode("utf-8")
-                g1 = re.search(r"^Sequence 1: [^ ]+ +(\d+) bp$", res, flags=re.MULTILINE)
-                refbp = float(g1.group(1))
-                g2 = re.search(r"^Sequence 2: [^ ]+ +(\d+) bp$", res, flags=re.MULTILINE)
-                subbp = float(g2.group(1))
-                g3 = re.search(r"^Sequences \(1:2\) Aligned\. Score: (\d+(\.\d+)?)$", res, flags=re.MULTILINE)
-                similarity = float(g3.group(1))
+        if not check_with_clustalw:
+            return ("sequence.fasta"+gz, seqlabel)
 
-                print(g1.group(0))
-                print(g2.group(0))
-                print(g3.group(0))
-            except Exception as e:
-                logging.warn("Error trying to QC against reference sequence using 'clustalw': %s", e)
+        with tempfile.NamedTemporaryFile() as tmp1:
+            with tempfile.NamedTemporaryFile() as tmp2:
+                refstring = pkg_resources.resource_string(__name__, "SARS-CoV-2-reference.fasta")
+                tmp1.write(refstring)
+                tmp1.flush()
+                tmp2.write(submitlabel.encode("utf8"))
+                tmp2.write(("".join(submitseq)).encode("utf8"))
+                tmp2.flush()
+                subbp = 0
+                refbp = 0
+                similarity = 0
+                try:
+                    cmd = ["minimap2", "-c", tmp1.name, tmp2.name]
+                    logging.info("QC checking similarity to reference")
+                    logging.info(" ".join(cmd))
+                    result = subprocess.run(cmd, stdout=subprocess.PIPE)
+                    result.check_returncode()
+                    res = result.stdout.decode("utf-8")
+                    mm = res.split("\t")
+                    if len(mm) >= 10:
+                        # divide Number of matching bases in the mapping / Target sequence length
+                        similarity = (float(mm[9]) / float(mm[6])) * 100.0
+                    else:
+                        similarity = 0
+                except Exception as e:
+                    logging.warn("QC against reference sequence using 'minimap2': %s", e, exc_info=e)
 
-            if refbp and (subbp/refbp) < .7:
-                raise ValueError("QC fail: submit sequence length is shorter than 70% reference")
-            if refbp and (subbp/refbp) > 1.3:
-                raise ValueError("QC fail: submit sequence length is greater than 130% reference")
-            if similarity and similarity < 70.0:
-                raise ValueError("QC fail: submit similarity is less than 70%")
-            if refbp == 0 or similarity == 0:
-                raise ValueError("QC fail")
+                if similarity and similarity < 70.0:
+                    raise ValueError("QC fail: alignment to reference was less than 70%% (was %2.2f%%)" % (similarity))
+                if similarity == 0:
+                    raise ValueError("QC fail")
 
         return ("sequence.fasta"+gz, seqlabel)
     elif seq_type == "text/fastq":
+        sequence.seek(0)
+        sequence.detach()
         return ("reads.fastq"+gz, seqlabel)
     else:
         raise ValueError("Sequence file does not look like a DNA FASTA or FASTQ")
diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py
index 9122ace..2b57991 100644
--- a/bh20sequploader/qc_metadata.py
+++ b/bh20sequploader/qc_metadata.py
@@ -21,20 +21,13 @@ def qc_metadata(metadatafile):
     shex = pkg_resources.resource_stream(__name__, "bh20seq-shex.rdf").read().decode("utf-8")
 
     if not isinstance(avsc_names, schema_salad.avro.schema.Names):
-        print(avsc_names)
-        return False
+        raise Exception(avsc_names)
 
-    try:
-        doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True)
-        g = schema_salad.jsonld_context.makerdf("workflow", doc, document_loader.ctx)
-        rslt, reason = evaluate(g, shex, doc["id"], "https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-shex.rdf#submissionShape")
+    doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True)
+    g = schema_salad.jsonld_context.makerdf("workflow", doc, document_loader.ctx)
+    rslt, reason = evaluate(g, shex, doc["id"], "https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-shex.rdf#submissionShape")
 
-        if not rslt:
-            log.debug(reason)
-            print(reason)
+    if not rslt:
+        raise Exception(reason)
 
-        return rslt
-    except Exception as e:
-        traceback.print_exc()
-        log.warn(e)
-    return False
+    return True
diff --git a/scripts/create_sra_metadata/SraExperimentPackage.2020.07.05.xml.gz b/scripts/create_sra_metadata/SraExperimentPackage.2020.07.05.xml.gz
new file mode 100644
index 0000000..88acb18
--- /dev/null
+++ b/scripts/create_sra_metadata/SraExperimentPackage.2020.07.05.xml.gz
diff --git a/scripts/download_sra_data/download_sra_data.py b/scripts/create_sra_metadata/create_sra_metadata.py
index 9145a43..ef0d119 100644
--- a/scripts/download_sra_data/download_sra_data.py
+++ b/scripts/create_sra_metadata/create_sra_metadata.py
@@ -8,9 +8,11 @@ import gzip
 
 dir_yaml = 'yaml'
 
-date = '2020.06.08'
+date = '2020.07.05'
 
-# Query on SRA: 'txid2697049[Organism]' (https://www.ncbi.nlm.nih.gov/sra/?term=txid2697049%5BOrganism%5D) -> Send to -> File -> Full XML -> Create File
+# Query on SRA: 'txid2697049[Organism]' (https://www.ncbi.nlm.nih.gov/sra/?term=txid2697049%5BOrganism%5D)
+# Query on SRA: 'txid2697049[Organism:noexp] NOT 0[Mbases ' (https://www.ncbi.nlm.nih.gov/sra/?term=txid2697049%5BOrganism:noexp%5D%20NOT%200[Mbases)
+#         -> Send to -> File -> Full XML -> Create File
 path_sra_metadata_xml = 'SraExperimentPackage.{}.xml.gz'.format(date)
 
 dir_dict_ontology_standardization = '../dict_ontology_standardization/'
@@ -70,14 +72,14 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
     accession = RUN.attrib['accession']
     run_accession_set.add(accession)
     #print(accession)
-    
+
     info_for_yaml_dict['sample']['sample_id'] = accession
     
-    SRAFiles = RUN.find('SRAFiles')
-    if SRAFiles is not None:
-        url = SRAFiles.find('SRAFile').attrib['url']
-        if 'sra-download.ncbi.nlm.nih.gov' in url:
-            run_accession_to_downloadble_file_url_dict[accession] = url
+    #SRAFiles = RUN.find('SRAFiles')
+    #if SRAFiles is not None:
+    #    url = SRAFiles.find('SRAFile').attrib['url']
+    #    if 'sra-download.ncbi.nlm.nih.gov' in url:
+    #        run_accession_to_downloadble_file_url_dict[accession] = url
   
 
     SAMPLE = EXPERIMENT_PACKAGE.find('SAMPLE')
@@ -90,6 +92,9 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
             VALUE_text = VALUE.text
 
             if TAG_text in ['host', 'host scientific name']:
+                if VALUE_text.lower() in ['homo sapien', 'homosapiens']:
+                    VALUE_text = 'Homo sapiens'
+
                 if VALUE_text in term_to_uri_dict:
                     info_for_yaml_dict['host']['host_species'] = term_to_uri_dict[VALUE_text]
                 else:
@@ -100,11 +105,19 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
                 elif VALUE_text.strip("'") not in ['missing', 'not collected', 'not provided']:
                     missing_value_list.append('\t'.join([accession, 'host_health_status', VALUE_text]))
             elif TAG_text in ['strain', 'isolate']:
-                if VALUE_text.lower() not in ['not applicable', 'missing', 'na', 'unknown']:
-                    if 'virus_strain' not in info_for_yaml_dict:
-                        info_for_yaml_dict['virus']['virus_strain'] = VALUE_text
+                if VALUE_text.lower() not in ['not applicable', 'missing', 'na', 'unknown', 'not provided']:
+                    value_to_insert = VALUE_text
+
+                    if value_to_insert.lower() in ['homo sapien', 'homosapiens']:
+                        value_to_insert = 'Homo sapiens'
+
+                    if value_to_insert in term_to_uri_dict:
+                        value_to_insert = term_to_uri_dict[value_to_insert]
+                        
+                    if 'virus_strain' not in info_for_yaml_dict:                        
+                        info_for_yaml_dict['virus']['virus_strain'] = value_to_insert
                     else:
-                        info_for_yaml_dict['virus']['virus_strain'] += '; ' + VALUE_text
+                        info_for_yaml_dict['virus']['virus_strain'] += '; ' + value_to_insert
             elif TAG_text in ['isolation_source', 'isolation source host-associated']:                    
                 if VALUE_text in term_to_uri_dict:
                     info_for_yaml_dict['sample']['specimen_source'] = [term_to_uri_dict[VALUE_text]]
@@ -179,17 +192,18 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
     
     EXPERIMENT = EXPERIMENT_PACKAGE.find('EXPERIMENT')
     INSTRUMENT_MODEL = [x.text for x in EXPERIMENT.find('PLATFORM').iter('INSTRUMENT_MODEL')][0]
+
     if INSTRUMENT_MODEL.lower() != 'unspecified':
         if INSTRUMENT_MODEL in term_to_uri_dict:
             info_for_yaml_dict['technology']['sample_sequencing_technology'] = [term_to_uri_dict[INSTRUMENT_MODEL]]
         else:
             missing_value_list.append('\t'.join([accession, 'sample_sequencing_technology', INSTRUMENT_MODEL]))
-    
+    #else:
+    #    print(accession, 'Missing INSTRUMENT_MODEL', info_for_yaml_dict)
     LIBRARY_DESCRIPTOR = EXPERIMENT.find('DESIGN').find('LIBRARY_DESCRIPTOR')
     if LIBRARY_DESCRIPTOR.text not in ['OTHER']:
         info_for_yaml_dict['technology']['additional_technology_information'] = 'LIBRARY_STRATEGY: {};'.format(LIBRARY_DESCRIPTOR.find('LIBRARY_STRATEGY').text)
-           
-            
+
     SUBMISSION = EXPERIMENT_PACKAGE.find('SUBMISSION')
     info_for_yaml_dict['submitter']['submitter_sample_id'] = SUBMISSION.attrib['accession']
     
@@ -197,7 +211,7 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
         info_for_yaml_dict['submitter']['originating_lab'] = SUBMISSION.attrib['lab_name']
 
     STUDY = EXPERIMENT_PACKAGE.find('STUDY')     
-    info_for_yaml_dict['submitter']['publication'] = SUBMISSION.attrib['lab_name']
+    info_for_yaml_dict['submitter']['publication'] = STUDY.attrib['alias']
     
     
     Organization = EXPERIMENT_PACKAGE.find('Organization')
@@ -222,6 +236,10 @@ for i, EXPERIMENT_PACKAGE in enumerate(EXPERIMENT_PACKAGE_SET):
         info_for_yaml_dict['sample']['collection_date'] = '1970-01-01'
         info_for_yaml_dict['sample']['additional_collection_information'] = "The real 'collection_date' is missing"
 
+    if 'sample_sequencing_technology' not in info_for_yaml_dict['technology']:
+        print(accession, ' - technology not found')
+        continue
+
     with open(os.path.join(dir_yaml, '{}.yaml'.format(accession)), 'w') as fw:
         json.dump(info_for_yaml_dict, fw, indent=2)
     
@@ -229,4 +247,4 @@ if len(missing_value_list) > 0:
     path_missing_terms_tsv = 'missing_terms.tsv'
     print('Written missing terms in {}'.format(path_missing_terms_tsv))
     with open(path_missing_terms_tsv, 'w') as fw:
-        fw.write('\n'.join(missing_value_list))
\ No newline at end of file
+        fw.write('\n'.join(missing_value_list))
diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv
index 204f7f2..4bea3ec 100644
--- a/scripts/dict_ontology_standardization/ncbi_countries.csv
+++ b/scripts/dict_ontology_standardization/ncbi_countries.csv
@@ -284,6 +284,7 @@ USA:CA,http://www.wikidata.org/entity/Q99
 USA: California,http://www.wikidata.org/entity/Q99
 USA:California,http://www.wikidata.org/entity/Q99
 "USA: CA, San Diego County",http://www.wikidata.org/entity/Q108143
+"USA: California, Monterey County",http://www.wikidata.org/entity/Q108072
 USA: CO,http://www.wikidata.org/entity/Q1261
 USA: CT,http://www.wikidata.org/entity/Q779
 USA: Connecticut,http://www.wikidata.org/entity/Q779
@@ -301,8 +302,9 @@ USA: IN,http://www.wikidata.org/entity/Q1415
 USA: KS,http://www.wikidata.org/entity/Q1558
 USA: KY,http://www.wikidata.org/entity/Q1603
 USA: LA,http://www.wikidata.org/entity/Q1588
-USA:Los Angeles,http://www.wikidata.org/entity/Q65
-"USA: New Orleans, LA",http://www.wikidata.org/entity/Q34404
+"USA: SLIDELL, LA, LA",https://www.wikidata.org/wiki/Q988156
+"USA: Slidell, LA, LA",https://www.wikidata.org/wiki/Q988156
+"USA: New Orleans, LA",https://www.wikidata.org/wiki/Q34404
 USA: MA,http://www.wikidata.org/entity/Q771
 USA: Massachusetts,http://www.wikidata.org/entity/Q771
 USA: MD,http://www.wikidata.org/entity/Q1391
@@ -336,6 +338,33 @@ USA: SC,http://www.wikidata.org/entity/Q1456
 USA: South Carolina,http://www.wikidata.org/entity/Q1456
 USA: SD,http://www.wikidata.org/entity/Q1211
 "USA: Snohomish County, WA",http://www.wikidata.org/entity/Q110403
+"USA: Washington,Snohomish County",http://www.wikidata.org/entity/Q110403
+"USA: Washington, Snohomish County",http://www.wikidata.org/entity/Q110403
+"USA: Washington,Skagit County",http://www.wikidata.org/entity/Q113892
+"USA: Washington, Skagit County",http://www.wikidata.org/entity/Q113892
+"USA: Washington,Pierce County",http://www.wikidata.org/entity/Q156459
+"USA: Washington, Pierce County",http://www.wikidata.org/entity/Q156459
+"USA: Washington,Mason County",http://www.wikidata.org/entity/Q111904
+"USA: Washington, Mason County",http://www.wikidata.org/entity/Q111904
+"USA: Washington,Kittitas County",http://www.wikidata.org/entity/Q111540
+"USA: Washington,King County",http://www.wikidata.org/entity/Q108861
+"USA: Washington, King County",http://www.wikidata.org/entity/Q108861
+"USA: King County,WA",http://www.wikidata.org/entity/Q108861
+"USA: Washington,Jefferson County",http://www.wikidata.org/entity/Q384737
+"USA: Washington,Grant County",http://www.wikidata.org/entity/Q281681
+"USA: Washington, Grant County",http://www.wikidata.org/entity/Q281681
+"USA: Washington,Franklin County",http://www.wikidata.org/entity/Q118716
+"USA: Washington, Franklin County",http://www.wikidata.org/entity/Q118716
+"USA: Washington,Clark County",http://www.wikidata.org/entity/Q156287
+"USA: Washington,Benton County",http://www.wikidata.org/entity/Q156216
+"USA: Washington, Benton County",http://www.wikidata.org/entity/Q156216
+"USA: Washington,Asotin County",http://www.wikidata.org/entity/Q156295
+"USA: Washington, Asotin County",http://www.wikidata.org/entity/Q156295
+"USA: Washington,Adams County",http://www.wikidata.org/entity/Q156273
+"USA: Washington, Adams County",http://www.wikidata.org/entity/Q156273
+"USA: Washington, Spokane County",http://www.wikidata.org/entity/Q485276
+"USA: Washington, Douglas County",http://www.wikidata.org/entity/Q156220
+"USA: Washington, Cowlitz County",http://www.wikidata.org/entity/Q156276
 USA: TN,http://www.wikidata.org/entity/Q1509
 USA: TX,http://www.wikidata.org/entity/Q1439
 USA: UT,http://www.wikidata.org/entity/Q829
@@ -347,6 +376,10 @@ USA: WA,http://www.wikidata.org/entity/Q1223
 USA: Washington,http://www.wikidata.org/entity/Q1223
 USA: WI,http://www.wikidata.org/entity/Q1537
 USA: Wisconsin,http://www.wikidata.org/entity/Q1537
+"USA: Washington,Yakima County",http://www.wikidata.org/entity/Q156629
+"USA: Washington, Yakima County",http://www.wikidata.org/entity/Q156629
+"USA: Washington,Whatcom County",http://www.wikidata.org/entity/Q156623
+"USA: Dane County, Wisconsin",http://www.wikidata.org/entity/Q502200
 USA: WV,http://www.wikidata.org/entity/Q1371
 USA: WY,http://www.wikidata.org/entity/Q1214
 Uzbekistan,http://www.wikidata.org/entity/Q265
diff --git a/scripts/dict_ontology_standardization/ncbi_host_species.csv b/scripts/dict_ontology_standardization/ncbi_host_species.csv
index bc6ac04..40572a3 100644
--- a/scripts/dict_ontology_standardization/ncbi_host_species.csv
+++ b/scripts/dict_ontology_standardization/ncbi_host_species.csv
@@ -5,5 +5,6 @@ sapiens,http://purl.obolibrary.org/obo/NCBITaxon_9606
 Mustela lutreola,http://purl.obolibrary.org/obo/NCBITaxon_9666
 Manis javanica,http://purl.obolibrary.org/obo/NCBITaxon_9974
 Felis catus,http://purl.obolibrary.org/obo/NCBITaxon_9685
+Felis catus; Domestic Shorthair,http://purl.obolibrary.org/obo/NCBITaxon_9685
 Panthera tigris jacksoni,http://purl.obolibrary.org/obo/NCBITaxon_419130
 Canis lupus familiaris,http://purl.obolibrary.org/obo/NCBITaxon_9615
diff --git a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv
index 964cbf3..59c4800 100644
--- a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv
+++ b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv
@@ -13,12 +13,14 @@ Illumina NextSeq 550,http://www.ebi.ac.uk/efo/EFO_0008566
 NextSeq550,http://www.ebi.ac.uk/efo/EFO_0008566
 NextSeq 550,http://www.ebi.ac.uk/efo/EFO_0008566
 Illumina MiniSeq,http://www.ebi.ac.uk/efo/EFO_0008636
+Illumina NovaSeq,http://www.ebi.ac.uk/efo/EFO_0008637
 Illumina NovaSeq 6000,http://www.ebi.ac.uk/efo/EFO_0008637
 Nanopore MinION,http://www.ebi.ac.uk/efo/EFO_0008632
 Oxford Nanopore MinION,http://www.ebi.ac.uk/efo/EFO_0008632
 ONT (Oxford Nanopore Technologies),http://purl.obolibrary.org/obo/NCIT_C146818
 Oxford Nanopore Technology,http://purl.obolibrary.org/obo/NCIT_C146818
 Oxford Nanopore technologies MinION,http://www.ebi.ac.uk/efo/EFO_0008632
+Oxford Nanopore Sequencing,http://purl.obolibrary.org/obo/NCIT_C146818
 MinION Oxford Nanopore,http://www.ebi.ac.uk/efo/EFO_0008632
 MinION,http://www.ebi.ac.uk/efo/EFO_0008632
 Nanopore,http://purl.obolibrary.org/obo/NCIT_C146818
@@ -33,3 +35,24 @@ ThermoFisher S5Plus,http://purl.obolibrary.org/obo/NCIT_C125894
 Sanger dideoxy sequencing,http://purl.obolibrary.org/obo/NCIT_C19641
 MGISEQ 2000,http://virtual-bh/MGISEQ2000
 MGISEQ2000,http://virtual-bh/MGISEQ2000
+Illumina HiSeq X,http://www.ebi.ac.uk/efo/EFO_0008567
+ONT GridION X5,http://www.ebi.ac.uk/efo/EFO_0008633
+ONT PremethION,http://www.ebi.ac.uk/efo/EFO_0008634
+PacBio RS II,http://www.ebi.ac.uk/efo/EFO_0008631
+PacBio Sequel System,http://www.ebi.ac.uk/efo/EFO_0008630
+Illumina Genome Analyzer,http://www.ebi.ac.uk/efo/EFO_0004200
+Illumina Genome Analyzer II,http://www.ebi.ac.uk/efo/EFO_0004201
+Illumina Genome Analyzer IIx,http://www.ebi.ac.uk/efo/EFO_0004202
+454 GS 20 sequencer,http://www.ebi.ac.uk/efo/EFO_0004206
+454 GS FLX Titanium sequencer,http://www.ebi.ac.uk/efo/EFO_0004433
+454 GS FLX sequencer,http://www.ebi.ac.uk/efo/EFO_0004432
+454 GS Junior sequencer,http://www.ebi.ac.uk/efo/EFO_0004434
+454 GS sequencer,http://www.ebi.ac.uk/efo/EFO_0004431
+AB SOLiD 4 System,http://www.ebi.ac.uk/efo/EFO_0004438
+AB SOLiD 4hq System,http://www.ebi.ac.uk/efo/EFO_0004441
+AB SOLiD 5500,http://www.ebi.ac.uk/efo/EFO_0004440
+AB SOLiD 5500xl,http://www.ebi.ac.uk/efo/EFO_0004436
+AB SOLiD PI System,http://www.ebi.ac.uk/efo/EFO_0004437
+AB SOLiD System,http://www.ebi.ac.uk/efo/EFO_0004435
+AB SOLiD System 2.0,http://www.ebi.ac.uk/efo/EFO_0004442
+AB SOLiD System 3.0,http://www.ebi.ac.uk/efo/EFO_0004439
diff --git a/scripts/docker/Dockerfile b/scripts/docker/Dockerfile
index 9fb33d5..02829d4 100644
--- a/scripts/docker/Dockerfile
+++ b/scripts/docker/Dockerfile
@@ -3,8 +3,8 @@ FROM debian:10
 RUN apt-get update && \
     apt-get -yq --no-install-recommends -o Acquire::Retries=6 install \
     python3 python3-pip python3-setuptools python3-dev python-pycurl \
-    clustalw python3-biopython libcurl4-openssl-dev build-essential \
+    minimap2 python3-biopython libcurl4-openssl-dev build-essential \
     libssl-dev libmagic-dev python3-magic && \
     apt-get clean
 
-RUN pip3 install bh20-seq-uploader
+RUN pip3 install bh20-seq-uploader py-dateutil
diff --git a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
index d76f56b..cb94787 100755
--- a/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
+++ b/scripts/download_genbank_data/from_genbank_to_fasta_and_yaml.py
@@ -4,6 +4,8 @@ import argparse
 parser = argparse.ArgumentParser()
 parser.add_argument('--skip-request', action='store_true', help='skip metadata and sequence request', required=False)
 parser.add_argument('--only-missing-id', action='store_true', help='download only missing id', required=False)
+parser.add_argument('--dict-ontology', type=str, help='where is the ontology',
+                    default='../dict_ontology_standardization/',required=False)
 args = parser.parse_args()
 
 from Bio import Entrez
@@ -22,7 +24,7 @@ num_ids_for_request = 100
 
 dir_metadata = 'metadata_from_nuccore'
 dir_fasta_and_yaml = 'fasta_and_yaml'
-dir_dict_ontology_standardization = '../dict_ontology_standardization/'
+dir_dict_ontology_standardization = args.dict_ontology
 
 today_date = date.today().strftime("%Y.%m.%d")
 path_ncbi_virus_accession = 'sequences.{}.acc'.format(today_date)
@@ -126,7 +128,7 @@ for path_dict_xxx_csv in [os.path.join(dir_dict_ontology_standardization, name_x
             if term in term_to_uri_dict:
                 print('Warning: in the dictionaries there are more entries for the same term ({}).'.format(term))
                 continue
-                
+
             term_to_uri_dict[term] = uri
 
 if not os.path.exists(dir_fasta_and_yaml):
@@ -171,7 +173,9 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
             # submitter info
             GBSeq_references = GBSeq.find('GBSeq_references')
             if GBSeq_references is not None:
-                info_for_yaml_dict['submitter']['authors'] = ["{}".format(x.text) for x in GBSeq_references.iter('GBAuthor')]
+                author_list = ["{}".format(x.text) for x in GBSeq_references.iter('GBAuthor')]
+                if len(author_list) > 0:
+                    info_for_yaml_dict['submitter']['authors'] = author_list
 
                 GBReference = GBSeq_references.find('GBReference')
                 if GBReference is not None:
@@ -220,7 +224,8 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
 
                                 new_seq_tec_list.append(seq_tec)
 
-                            info_for_yaml_dict['technology']['sample_sequencing_technology'] = [x for x in new_seq_tec_list]
+                            if len(new_seq_tec_list) > 0:
+                                info_for_yaml_dict['technology']['sample_sequencing_technology'] = [x for x in new_seq_tec_list]
                         else:
                             info_for_yaml_dict['technology'][field_in_yaml] = tech_info_to_parse
 
@@ -238,58 +243,62 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
                     GBQualifier_name_text = GBQualifier.find('GBQualifier_name').text
 
                     if GBQualifier_name_text == 'host':
-                        GBQualifier_value_text_list = GBQualifier_value_text.split('; ')
-
-                        if GBQualifier_value_text_list[0] in term_to_uri_dict:
-                            info_for_yaml_dict['host']['host_species'] = term_to_uri_dict[GBQualifier_value_text_list[0]]
-                        elif GBQualifier_value_text_list[0] and ('MT215193' in accession_version or 'MT270814' in accession_version):
-                            # Information checked manually from NCBI Virus
-                            info_for_yaml_dict['host']['host_species'] = term_to_uri_dict['Canis lupus familiaris']
+                        if GBQualifier_value_text in term_to_uri_dict:
+                            # Cases like 'Felis catus; Domestic Shorthair'
+                            info_for_yaml_dict['host']['host_species'] = term_to_uri_dict[GBQualifier_value_text]
                         else:
-                            missing_value_list.append('\t'.join([accession_version, 'host_species', GBQualifier_value_text_list[0]]))
-
-                        # Possible cases:
-                        # - Homo sapiens						--> ['Homo sapiens']
-                        # - Homo sapiens; female				--> ['Homo sapiens', 'female']
-                        # - Homo sapiens; female 63				--> ['Homo sapiens', 'female 63']
-                        # - Homo sapiens; female; age 40		--> ['Homo sapiens', 'female', 'age 40']
-                        # - Homo sapiens; gender: F; age: 61	--> ['Homo sapiens', 'gender: F', 'age: 61']
-                        # - Homo sapiens; gender: M; age: 68	--> ['Homo sapiens', 'gender: M', 'age: 68']
-                        # - Homo sapiens; hospitalized patient	--> ['Homo sapiens', 'hospitalized patient']
-                        # - Homo sapiens; male					--> ['Homo sapiens', 'male']
-                        # - Homo sapiens; male; 63				--> ['Homo sapiens', 'male', '63']
-                        # - Homo sapiens; male; age 29			--> ['Homo sapiens', 'male', 'age 29']
-                        # - Homo sapiens; symptomatic			--> ['Homo sapiens', 'symptomatic']
-                        if len(GBQualifier_value_text_list) > 1:
-                            host_sex = ''
-                            if 'female' in GBQualifier_value_text_list[1]:
-                                host_sex = 'female'
-                            elif 'male' in GBQualifier_value_text_list[1]:
-                                host_sex = 'male'
-                            elif 'gender' in GBQualifier_value_text_list[1]:
-                                host_sex_one_lecter = GBQualifier_value_text_list[1].split(':')[-1].strip()
-                                if host_sex_one_lecter in ['F', 'M']:
-                                    host_sex = 'female' if host_sex_one_lecter == 'F' else 'male'
-
-                            if host_sex in ['male', 'female']:
-                                info_for_yaml_dict['host']['host_sex'] = "http://purl.obolibrary.org/obo/PATO_0000384" if host_sex == 'male' else "http://purl.obolibrary.org/obo/PATO_0000383"
-                            elif GBQualifier_value_text_list[1] in term_to_uri_dict:
-                                info_for_yaml_dict['host']['host_health_status'] = term_to_uri_dict[GBQualifier_value_text_list[1]]                            
+                            GBQualifier_value_text_list = GBQualifier_value_text.split('; ')
+
+                            if GBQualifier_value_text_list[0] in term_to_uri_dict:
+                                info_for_yaml_dict['host']['host_species'] = term_to_uri_dict[GBQualifier_value_text_list[0]]
+                            elif GBQualifier_value_text_list[0] and ('MT215193' in accession_version or 'MT270814' in accession_version):
+                                # Information checked manually from NCBI Virus
+                                info_for_yaml_dict['host']['host_species'] = term_to_uri_dict['Canis lupus familiaris']
                             else:
-                                missing_value_list.append('\t'.join([accession_version, 'host_sex or host_health_status', GBQualifier_value_text_list[1]]))
-
-                            # Host age
-                            host_age = -1
-                            if len(GBQualifier_value_text_list[1].split(' ')) > 1 and is_integer(GBQualifier_value_text_list[1].split(' ')[-1]):
-                                host_age = int(GBQualifier_value_text_list[1].split(' ')[-1])
-                            elif len(GBQualifier_value_text_list) > 2 and is_integer(GBQualifier_value_text_list[2].split(' ')[-1]):
-                                host_age = int(GBQualifier_value_text_list[2].split(' ')[-1])
-
-                            if host_age > -1:
-                                info_for_yaml_dict['host']['host_age'] = host_age
-                                info_for_yaml_dict['host']['host_age_unit'] = 'http://purl.obolibrary.org/obo/UO_0000036'
-                            elif len(GBQualifier_value_text_list) > 2:
-                                missing_value_list.append('\t'.join([accession_version, 'host_age', GBQualifier_value_text_list[2]]))
+                                missing_value_list.append('\t'.join([accession_version, 'host_species', GBQualifier_value_text_list[0]]))
+
+                            # Possible cases:
+                            # - Homo sapiens						--> ['Homo sapiens']
+                            # - Homo sapiens; female				--> ['Homo sapiens', 'female']
+                            # - Homo sapiens; female 63				--> ['Homo sapiens', 'female 63']
+                            # - Homo sapiens; female; age 40		--> ['Homo sapiens', 'female', 'age 40']
+                            # - Homo sapiens; gender: F; age: 61	--> ['Homo sapiens', 'gender: F', 'age: 61']
+                            # - Homo sapiens; gender: M; age: 68	--> ['Homo sapiens', 'gender: M', 'age: 68']
+                            # - Homo sapiens; hospitalized patient	--> ['Homo sapiens', 'hospitalized patient']
+                            # - Homo sapiens; male					--> ['Homo sapiens', 'male']
+                            # - Homo sapiens; male; 63				--> ['Homo sapiens', 'male', '63']
+                            # - Homo sapiens; male; age 29			--> ['Homo sapiens', 'male', 'age 29']
+                            # - Homo sapiens; symptomatic			--> ['Homo sapiens', 'symptomatic']
+                            if len(GBQualifier_value_text_list) > 1:
+                                host_sex = ''
+                                if 'female' in GBQualifier_value_text_list[1]:
+                                    host_sex = 'female'
+                                elif 'male' in GBQualifier_value_text_list[1]:
+                                    host_sex = 'male'
+                                elif 'gender' in GBQualifier_value_text_list[1]:
+                                    host_sex_one_lecter = GBQualifier_value_text_list[1].split(':')[-1].strip()
+                                    if host_sex_one_lecter in ['F', 'M']:
+                                        host_sex = 'female' if host_sex_one_lecter == 'F' else 'male'
+
+                                if host_sex in ['male', 'female']:
+                                    info_for_yaml_dict['host']['host_sex'] = "http://purl.obolibrary.org/obo/PATO_0000384" if host_sex == 'male' else "http://purl.obolibrary.org/obo/PATO_0000383"
+                                elif GBQualifier_value_text_list[1] in term_to_uri_dict:
+                                    info_for_yaml_dict['host']['host_health_status'] = term_to_uri_dict[GBQualifier_value_text_list[1]]
+                                else:
+                                    missing_value_list.append('\t'.join([accession_version, 'host_sex or host_health_status', GBQualifier_value_text_list[1]]))
+
+                                # Host age
+                                host_age = -1
+                                if len(GBQualifier_value_text_list[1].split(' ')) > 1 and is_integer(GBQualifier_value_text_list[1].split(' ')[-1]):
+                                    host_age = int(GBQualifier_value_text_list[1].split(' ')[-1])
+                                elif len(GBQualifier_value_text_list) > 2 and is_integer(GBQualifier_value_text_list[2].split(' ')[-1]):
+                                    host_age = int(GBQualifier_value_text_list[2].split(' ')[-1])
+
+                                if host_age > -1:
+                                    info_for_yaml_dict['host']['host_age'] = host_age
+                                    info_for_yaml_dict['host']['host_age_unit'] = 'http://purl.obolibrary.org/obo/UO_0000036'
+                                elif len(GBQualifier_value_text_list) > 2:
+                                    missing_value_list.append('\t'.join([accession_version, 'host_age', GBQualifier_value_text_list[2]]))
                     elif GBQualifier_name_text == 'collected_by':
                         if any([x in GBQualifier_value_text.lower() for x in ['institute', 'hospital', 'city', 'center']]):
                             info_for_yaml_dict['sample']['collecting_institution'] = GBQualifier_value_text
@@ -362,9 +371,9 @@ for path_metadata_xxx_xml in [os.path.join(dir_metadata, name_metadata_xxx_xml)
                         info_for_yaml_dict['virus']['virus_species'] = "http://purl.obolibrary.org/obo/NCBITaxon_"+GBQualifier_value_text.split('taxon:')[1]
 
 
-            # Remove technology key if empty!
-            if (info_for_yaml_dict['technology']=={}):
-                del info_for_yaml_dict['technology']
+            if 'sample_sequencing_technology' not in info_for_yaml_dict['technology']:
+                print(accession_version, ' - technology not found')
+                continue
 
             with open(os.path.join(dir_fasta_and_yaml, '{}.fasta'.format(accession_version)), 'w') as fw:
                 fw.write('>{}\n{}'.format(accession_version, GBSeq_sequence.text.upper()))
@@ -391,5 +400,5 @@ if len(accession_with_errors_list) > 0:
     print('Written the accession with errors in {}'.format(path_accession_with_errors_tsv))
     with open(path_accession_with_errors_tsv, 'w') as fw:
         fw.write('\n'.join(accession_with_errors_list))
-        
+
 print('Num. new sequences with length >= {} bp: {}'.format(min_len_to_count, num_seq_with_len_ge_X_bp))
diff --git a/scripts/download_sra_data/SraExperimentPackage.2020.06.08.xml.gz b/scripts/download_sra_data/SraExperimentPackage.2020.06.08.xml.gz
deleted file mode 100644
index f9cd995..0000000
--- a/scripts/download_sra_data/SraExperimentPackage.2020.06.08.xml.gz
+++ /dev/null
diff --git a/scripts/fetch_from_genbank.cwl b/scripts/fetch_from_genbank.cwl
new file mode 100644
index 0000000..45c8eec
--- /dev/null
+++ b/scripts/fetch_from_genbank.cwl
@@ -0,0 +1,49 @@
+cwlVersion: v1.1
+class: CommandLineTool
+inputs:
+  importScript:
+    type: File
+    default:
+      class: File
+      location: download_genbank_data/from_genbank_to_fasta_and_yaml.py
+    inputBinding: {position: 1}
+  dict:
+    type: Directory
+    inputBinding:
+      prefix: --dict-ontology
+      position: 2
+    default:
+      class: Directory
+      location: dict_ontology_standardization
+  existing_metadata_from_nuccore:
+    type: Directory?
+    inputBinding:
+      valueFrom: "--skip-request"
+      position: 3
+outputs:
+  fasta_and_yaml:
+    type: Directory
+    outputBinding:
+      glob: fasta_and_yaml
+  metadata_from_nuccore:
+    type: Directory
+    outputBinding:
+      glob: metadata_from_nuccore
+  accessions:
+    type: File?
+    outputBinding:
+      glob: "*.acc"
+  missing_terms:
+    type: File
+    outputBinding:
+      glob: missing_terms.tsv
+requirements:
+  InitialWorkDirRequirement:
+    listing:
+      - entry: $(inputs.existing_metadata_from_nuccore)
+        entryname: metadata_from_nuccore
+  DockerRequirement:
+    dockerPull: bh20-seq-uploader/import
+  NetworkAccess:
+    networkAccess: true
+baseCommand: python3
diff --git a/scripts/import.cwl b/scripts/import.cwl
index d84516b..4b4b8ca 100644
--- a/scripts/import.cwl
+++ b/scripts/import.cwl
@@ -12,7 +12,7 @@ inputs:
     type: File
     default:
       class: File
-      location: from_genbank_to_fasta_and_yaml.py
+      location: download_genbank_data/from_genbank_to_fasta_and_yaml.py
     inputBinding: {position: 2}
   dict:
     type: Directory
diff --git a/scripts/import_from_genbank.cwl b/scripts/import_from_genbank.cwl
new file mode 100644
index 0000000..dcf9acb
--- /dev/null
+++ b/scripts/import_from_genbank.cwl
@@ -0,0 +1,27 @@
+cwlVersion: v1.1
+class: Workflow
+inputs:
+  existing_metadata_from_nuccore:
+    type: Directory?
+outputs: []
+requirements:
+  ScatterFeatureRequirement: {}
+steps:
+  fetch_from_genbank:
+    in:
+      existing_metadata_from_nuccore: existing_metadata_from_nuccore
+    out: [fasta_and_yaml, metadata_from_nuccore, accessions]
+    run: fetch_from_genbank.cwl
+  split_into_arrays:
+    in:
+      dir: fetch_from_genbank/fasta_and_yaml
+    out: [fasta, metadata]
+    run: split_into_arrays.cwl
+  upload:
+    in:
+      fasta: split_into_arrays/fasta
+      metadata: split_into_arrays/metadata
+    out: []
+    scatter: [fasta, metadata]
+    scatterMethod: dotproduct
+    run: upload.cwl
diff --git a/scripts/import_to_arvados.py b/scripts/import_to_arvados.py
index 78cd13d..aca72d6 100644
--- a/scripts/import_to_arvados.py
+++ b/scripts/import_to_arvados.py
@@ -11,4 +11,4 @@ os.chdir("fasta_and_yaml")
 fasta_files = glob.glob("*.fasta")
 
 for f in fasta_files:
-    subprocess.run(["bh20-seq-uploader", f, "%s.yaml" %f[:-6]])
+    subprocess.run(["bh20-seq-uploader", "%s.yaml" %f[:-6], f])
diff --git a/scripts/split_into_arrays.cwl b/scripts/split_into_arrays.cwl
new file mode 100644
index 0000000..102fe7d
--- /dev/null
+++ b/scripts/split_into_arrays.cwl
@@ -0,0 +1,30 @@
+cwlVersion: v1.1
+class: ExpressionTool
+requirements:
+  InlineJavascriptRequirement: {}
+inputs:
+  dir:
+    type: Directory
+    loadListing: shallow_listing
+outputs:
+  fasta: File[]
+  metadata: File[]
+expression: |
+  ${
+  var dir = inputs.dir;
+  var fasta = [];
+  var metadata = [];
+  dir.listing.sort(function(a, b) { return a.basename < b.basename; });
+  for (var i = 0; i < dir.listing.length; i++) {
+    if (dir.listing[i].basename.substr(-6) == ".fasta") {
+      fasta.push(dir.listing[i]);
+    }
+    if (dir.listing[i].basename.substr(-5) == ".yaml") {
+      metadata.push(dir.listing[i]);
+    }
+  }
+  if (fasta.length != metadata.length) {
+    throw "They dont match";
+  }
+  return {"fasta": fasta, "metadata": metadata};
+  }
diff --git a/scripts/upload.cwl b/scripts/upload.cwl
new file mode 100644
index 0000000..0fed09a
--- /dev/null
+++ b/scripts/upload.cwl
@@ -0,0 +1,13 @@
+cwlVersion: v1.1
+class: CommandLineTool
+inputs:
+  fasta: File
+  metadata: File
+outputs: []
+requirements:
+  DockerRequirement:
+    dockerPull: bh20-seq-uploader/import
+  NetworkAccess:
+    networkAccess: true
+baseCommand: bh20-seq-uploader
+arguments: [--skip-qc, $(inputs.metadata), $(inputs.fasta)]
diff --git a/semantic_enrichment/labels.ttl b/semantic_enrichment/labels.ttl
index 5d96c5b..68c21bc 100644
--- a/semantic_enrichment/labels.ttl
+++ b/semantic_enrichment/labels.ttl
@@ -38,6 +38,7 @@
 <http://purl.obolibrary.org/obo/OBI_0000759> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina" .
 <http://purl.obolibrary.org/obo/NCIT_C125894> <http://www.w3.org/2000/01/rdf-schema#label> "Ion Semiconductor Sequencing".
 <http://purl.obolibrary.org/obo/NCIT_C19641> <http://www.w3.org/2000/01/rdf-schema#label> "Dideoxy Chain Termination DNA Sequencing" .
+<http://www.ebi.ac.uk/efo/EFO_0008567> <http://www.w3.org/2000/01/rdf-schema#label> "Illumina HiSeq X" .
 <http://purl.obolibrary.org/obo/NCIT_C155831> <http://www.w3.org/2000/01/rdf-schema#label> "Nasopharyngeal Swab Specimen" .
 <http://purl.obolibrary.org/obo/NCIT_C155835> <http://www.w3.org/2000/01/rdf-schema#label> "Oropharyngeal Swab Specimen" .
 <http://purl.obolibrary.org/obo/NCIT_C13195> <http://www.w3.org/2000/01/rdf-schema#label> "Bronchoalveolar Lavage Fluid" .
@@ -46,4 +47,4 @@
 <http://purl.obolibrary.org/obo/NCIT_C13234> <http://www.w3.org/2000/01/rdf-schema#label> "Feces" .
 <http://purl.obolibrary.org/obo/NCIT_C13325> <http://www.w3.org/2000/01/rdf-schema#label> "Serum" .
 <http://purl.obolibrary.org/obo/NCIT_C13275> <http://www.w3.org/2000/01/rdf-schema#label> "Saliva" .
-<http://purl.obolibrary.org/obo/NCIT_C132119> <http://www.w3.org/2000/01/rdf-schema#label> "Nasal Swab" .
\ No newline at end of file
+<http://purl.obolibrary.org/obo/NCIT_C132119> <http://www.w3.org/2000/01/rdf-schema#label> "Nasal Swab" .