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-rw-r--r--bh20seqanalyzer/main.py71
-rw-r--r--bh20sequploader/main.py58
-rw-r--r--bh20sequploader/qc_fasta.py35
-rw-r--r--scripts/dict_ontology_standardization/ncbi_countries.csv32
-rw-r--r--scripts/dict_ontology_standardization/ncbi_host_species.csv2
-rw-r--r--scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv7
-rw-r--r--scripts/dict_ontology_standardization/ncbi_speciesman_source.csv1
-rw-r--r--scripts/docker/Dockerfile4
-rw-r--r--workflows/fastq2fasta/bam2fasta.cwl2
-rw-r--r--workflows/fastq2fasta/bcftools-consensus.cwl9
-rw-r--r--workflows/fastq2fasta/bcftools-view-qc.cwl2
-rw-r--r--workflows/fastq2fasta/fastq2fasta.cwl2
12 files changed, 161 insertions, 64 deletions
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py
index 31ad4c4..9a36cae 100644
--- a/bh20seqanalyzer/main.py
+++ b/bh20seqanalyzer/main.py
@@ -30,6 +30,7 @@ def validate_upload(api, collection, validated_project,
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:
@@ -39,21 +40,25 @@ def validate_upload(api, collection, validated_project,
logging.warn("Failed metadata qc")
if valid:
- tgt = None
- for n in ("sequence.fasta", "reads.fastq"):
- if n not in col:
- continue
- with col.open(n) as qf:
- tgt = qc_fasta(qf)
- if tgt != n:
- logging.info("Expected %s but magic says it should be %s", n, tgt)
- valid = False
- elif tgt == "reads.fastq":
- start_fastq_to_fasta(api, collection, fastq_project, fastq_workflow_uuid)
- return False
- if tgt is None:
+ try:
+ tgt = None
+ paired = {"reads_1.fastq": "reads.fastq", "reads_1.fastq.gz": "reads.fastq.gz"}
+ for n in ("sequence.fasta", "reads.fastq", "reads.fastq.gz", "reads_1.fastq", "reads_1.fastq.gz"):
+ if n not in col:
+ continue
+ 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
+ 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
- logging.warn("Upload '%s' does not contain sequence.fasta or reads.fastq", collection["name"])
dup = api.collections().list(filters=[["owner_uuid", "=", validated_project],
["portable_data_hash", "=", col.portable_data_hash()]]).execute()
@@ -69,9 +74,8 @@ def validate_upload(api, collection, validated_project,
"owner_uuid": validated_project,
"name": "%s (%s)" % (collection["name"], time.asctime(time.gmtime()))}).execute()
else:
- pass
# It is invalid, delete it.
- #logging.warn("Deleting '%s'" % collection["name"])
+ logging.warn("Suggest deleting '%s'" % collection["name"])
#api.collections().delete(uuid=collection["uuid"]).execute()
return valid
@@ -95,6 +99,7 @@ def run_workflow(api, parent_project, workflow_uuid, name, inputobj):
tmp.name]
logging.info("Running %s" % ' '.join(cmd))
comp = subprocess.run(cmd, capture_output=True)
+ logging.info("Submitted %s", comp.stdout)
if comp.returncode != 0:
logging.error(comp.stderr.decode('utf-8'))
@@ -103,12 +108,11 @@ def run_workflow(api, parent_project, workflow_uuid, name, inputobj):
def start_fastq_to_fasta(api, collection,
analysis_project,
- fastq_workflow_uuid):
- newproject = run_workflow(api, analysis_project, fastq_workflow_uuid, "FASTQ to FASTA", {
- "fastq_forward": {
- "class": "File",
- "location": "keep:%s/reads.fastq" % collection["portable_data_hash"]
- },
+ fastq_workflow_uuid,
+ tgt,
+ sample_id):
+
+ params = {
"metadata": {
"class": "File",
"location": "keep:%s/metadata.yaml" % collection["portable_data_hash"]
@@ -116,8 +120,26 @@ def start_fastq_to_fasta(api, collection,
"ref_fasta": {
"class": "File",
"location": "keep:ffef6a3b77e5e04f8f62a7b6f67264d1+556/SARS-CoV2-NC_045512.2.fasta"
+ },
+ "sample_id": sample_id
+ }
+
+ if tgt.startswith("reads.fastq"):
+ params["fastq_forward"] = {
+ "class": "File",
+ "location": "keep:%s/%s" % (collection["portable_data_hash"], tgt)
+ }
+ elif tgt.startswith("reads_1.fastq"):
+ params["fastq_forward"] = {
+ "class": "File",
+ "location": "keep:%s/reads_1.%s" % (collection["portable_data_hash"], tgt[8:])
}
- })
+ params["fastq_reverse"] = {
+ "class": "File",
+ "location": "keep:%s/reads_2.%s" % (collection["portable_data_hash"], tgt[8:])
+ }
+
+ newproject = run_workflow(api, analysis_project, fastq_workflow_uuid, "FASTQ to FASTA", params)
api.collections().update(uuid=collection["uuid"],
body={"owner_uuid": newproject["uuid"]}).execute()
@@ -222,6 +244,7 @@ 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('--once', action="store_true")
args = parser.parse_args()
api = arvados.api()
@@ -265,4 +288,6 @@ def main():
args.pangenome_analysis_project,
args.latest_result_collection)
+ if args.once:
+ break
time.sleep(15)
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index a2e62fa..c442af0 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -22,18 +22,10 @@ ARVADOS_API_HOST='lugli.arvadosapi.com'
ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
UPLOAD_PROJECT='lugli-j7d0g-n5clictpuvwk8aa'
-def main():
- parser = argparse.ArgumentParser(description='Upload SARS-CoV-19 sequences for analysis')
- parser.add_argument('sequence', type=argparse.FileType('r'), help='sequence FASTA/FASTQ')
- parser.add_argument('metadata', type=argparse.FileType('r'), help='sequence metadata json')
- parser.add_argument("--validate", action="store_true", help="Dry run, validate only")
- args = parser.parse_args()
-
- api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True)
-
+def qa_stuff(metadata, sequence_p1, sequence_p2):
try:
log.debug("Checking metadata")
- if not qc_metadata(args.metadata.name):
+ if not qc_metadata(metadata.name):
log.warning("Failed metadata qc")
exit(1)
except ValueError as e:
@@ -42,29 +34,52 @@ def main():
print(e)
exit(1)
+ target = []
try:
- log.debug("Checking FASTA QC")
- target = qc_fasta(args.sequence)
+ log.debug("Checking FASTA/FASTQ QC")
+ target.append(qc_fasta(sequence_p1))
+ 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:
log.debug(e)
log.debug("Failed FASTA qc")
print(e)
exit(1)
+ return target
+
+def upload_sequence(col, target, sequence):
+ with col.open(target[0], "wb") as f:
+ r = sequence.read(65536)
+ while r:
+ f.write(r)
+ r = sequence.read(65536)
+
+
+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("--validate", action="store_true", help="Dry run, validate only")
+ 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)
+ seqlabel = target[0][1]
+
if args.validate:
print("Valid")
exit(0)
col = arvados.collection.Collection(api_client=api)
- with col.open(target, "w") as f:
- r = args.sequence.read(65536)
- seqlabel = r[1:r.index("\n")]
- print(seqlabel)
- while r:
- f.write(r)
- r = args.sequence.read(65536)
- args.sequence.close()
+ upload_sequence(col, target[0], args.sequence_p1)
+ if args.sequence_p2:
+ upload_sequence(col, target[1], args.sequence_p2)
print("Reading metadata")
with col.open("metadata.yaml", "w") as f:
@@ -73,7 +88,6 @@ def main():
while r:
f.write(r)
r = args.metadata.read(65536)
- args.metadata.close()
external_ip = urllib.request.urlopen('https://ident.me').read().decode('utf8')
@@ -93,6 +107,8 @@ def main():
(seqlabel, properties['upload_user'], properties['upload_ip']),
properties=properties, ensure_unique_name=True)
+ print("Saved to %s" % col.manifest_locator())
+
print("Done")
if __name__ == "__main__":
diff --git a/bh20sequploader/qc_fasta.py b/bh20sequploader/qc_fasta.py
index 5c8cf3a..e198430 100644
--- a/bh20sequploader/qc_fasta.py
+++ b/bh20sequploader/qc_fasta.py
@@ -5,6 +5,8 @@ import subprocess
import tempfile
import logging
import re
+import io
+import gzip
log = logging.getLogger(__name__ )
@@ -23,7 +25,7 @@ def read_fasta(sequence):
raise ValueError("FASTA file contains multiple entries")
return label, bases
-def qc_fasta(sequence):
+def qc_fasta(arg_sequence):
log.debug("Starting qc_fasta")
schema_resource = pkg_resources.resource_stream(__name__, "validation/formats")
with tempfile.NamedTemporaryFile() as tmp:
@@ -31,12 +33,24 @@ def qc_fasta(sequence):
tmp.flush()
val = magic.Magic(magic_file=tmp.name,
uncompress=False, mime=True)
- seq_type = val.from_buffer(sequence.read(4096)).lower()
+
+ gz = ""
+ if arg_sequence.name.endswith(".gz"):
+ sequence = gzip.GzipFile(fileobj=arg_sequence, mode='rb')
+ gz = ".gz"
+ else:
+ sequence = arg_sequence
+
+ sequence = io.TextIOWrapper(sequence)
+ r = sequence.read(4096)
sequence.seek(0)
+
+ seqlabel = r[1:r.index("\n")]
+ seq_type = val.from_buffer(r).lower()
+
if seq_type == "text/fasta":
# ensure that contains only one entry
submitlabel, submitseq = read_fasta(sequence)
- sequence.seek(0)
with tempfile.NamedTemporaryFile() as tmp1:
refstring = pkg_resources.resource_string(__name__, "SARS-CoV-2-reference.fasta")
@@ -44,6 +58,9 @@ def qc_fasta(sequence):
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"]
@@ -64,15 +81,17 @@ def qc_fasta(sequence):
except Exception as e:
logging.warn("Error trying to QC against reference sequence using 'clustalw': %s", e)
- if (subbp/refbp) < .7:
+ if refbp and (subbp/refbp) < .7:
raise ValueError("QC fail: submit sequence length is shorter than 70% reference")
- if (subbp/refbp) > 1.3:
+ if refbp and (subbp/refbp) > 1.3:
raise ValueError("QC fail: submit sequence length is greater than 130% reference")
- if similarity < 70.0:
+ 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")
- return "sequence.fasta"
+ return ("sequence.fasta"+gz, seqlabel)
elif seq_type == "text/fastq":
- return "reads.fastq"
+ return ("reads.fastq"+gz, seqlabel)
else:
raise ValueError("Sequence file does not look like a DNA FASTA or FASTQ")
diff --git a/scripts/dict_ontology_standardization/ncbi_countries.csv b/scripts/dict_ontology_standardization/ncbi_countries.csv
index 7e83564..85d4e8a 100644
--- a/scripts/dict_ontology_standardization/ncbi_countries.csv
+++ b/scripts/dict_ontology_standardization/ncbi_countries.csv
@@ -12,6 +12,9 @@ Armenia,http://www.wikidata.org/entity/Q399
Australia,http://www.wikidata.org/entity/Q408
Australia: Queensland,http://www.wikidata.org/entity/Q36074
Australia: Victoria,http://www.wikidata.org/entity/Q36687
+"Australia: Melbourne, Victoria",http://www.wikidata.org/entity/Q3141
+Australia: Northern Territory,http://www.wikidata.org/entity/Q3235
+Australia: NSW,http://www.wikidata.org/entity/Q3224
Austria,http://www.wikidata.org/entity/Q40
Azerbaijan,http://www.wikidata.org/entity/Q227
Bahrain,http://www.wikidata.org/entity/Q398
@@ -31,8 +34,10 @@ Bulgaria,http://www.wikidata.org/entity/Q219
Burkina Faso,http://www.wikidata.org/entity/Q965
Burundi,http://www.wikidata.org/entity/Q967
Cambodia,http://www.wikidata.org/entity/Q424
+Cambodia:Sihanoukville,http://www.wikidata.org/entity/Q18207676
Cameroon,http://www.wikidata.org/entity/Q1009
Canada,http://www.wikidata.org/entity/Q16
+Canada: Toronto,http://www.wikidata.org/entity/Q172
Cape Verde,http://www.wikidata.org/entity/Q1011
Central African Republic,http://www.wikidata.org/entity/Q929
Chad,http://www.wikidata.org/entity/Q657
@@ -65,12 +70,13 @@ China: Jiangxi,http://www.wikidata.org/entity/Q57052
China: Jilin,http://www.wikidata.org/entity/Q45208
China: Liaoning,http://www.wikidata.org/entity/Q43934
China: Macau,http://www.wikidata.org/entity/Q14773
-China: Nanchang,https://www.wikidata.org/wiki/Q171943
+China: Nanchang,http://www.wikidata.org/entity/Q171943
China: Ningxia Hui Autonomous Region,http://www.wikidata.org/entity/Q57448
China: Qinghai,http://www.wikidata.org/entity/Q45833
China: Shaanxi,http://www.wikidata.org/entity/Q47974
China: Shandong,http://www.wikidata.org/entity/Q43407
China: Shanghai,http://www.wikidata.org/entity/Q8686
+China:Shanghai,http://www.wikidata.org/entity/Q8686
China: Shanxi,http://www.wikidata.org/entity/Q46913
China: Shenzhen,http://www.wikidata.org/entity/Q15174
China: Sichuan,http://www.wikidata.org/entity/Q19770
@@ -111,11 +117,13 @@ France,http://www.wikidata.org/entity/Q142
Gabon,http://www.wikidata.org/entity/Q1000
Georgia,http://www.wikidata.org/entity/Q230
Germany,http://www.wikidata.org/entity/Q183
-Germany: Bavaria,https://www.wikidata.org/wiki/Q980
-Germany: Dusseldorf,https://www.wikidata.org/wiki/Q1718
+Germany: Bavaria,http://www.wikidata.org/entity/Q980
+Germany: Dusseldorf,http://www.wikidata.org/entity/Q1718
+Germany: Heinsberg,http://www.wikidata.org/entity/Q14833
+Germany: Starnberg,http://www.wikidata.org/entity/Q61936
Ghana,http://www.wikidata.org/entity/Q117
Greece,http://www.wikidata.org/entity/Q41
-Greece: Athens,https://www.wikidata.org/wiki/Q1524
+Greece: Athens,http://www.wikidata.org/entity/Q1524
Grenada,http://www.wikidata.org/entity/Q769
Guatemala,http://www.wikidata.org/entity/Q774
Guinea,http://www.wikidata.org/entity/Q1006
@@ -139,8 +147,8 @@ Ireland,http://www.wikidata.org/entity/Q27
Israel,http://www.wikidata.org/entity/Q801
Italy,http://www.wikidata.org/entity/Q38
Italy: Cagliari,http://www.wikidata.org/entity/Q1897
-Italy: Lazio,https://www.wikidata.org/wiki/Q1282
-Italy: Palermo,https://www.wikidata.org/wiki/Q2656
+Italy: Lazio,http://www.wikidata.org/entity/Q1282
+Italy: Palermo,http://www.wikidata.org/entity/Q2656
Italy: Rome,http://www.wikidata.org/entity/Q220
Ivory Coast,http://www.wikidata.org/entity/Q1008
Jamaica,http://www.wikidata.org/entity/Q766
@@ -181,7 +189,7 @@ Mozambique,http://www.wikidata.org/entity/Q1029
Myanmar,http://www.wikidata.org/entity/Q836
Namibia,http://www.wikidata.org/entity/Q1030
Nauru,http://www.wikidata.org/entity/Q697
-Netherlands: Milheeze,https://www.wikidata.org/wiki/Q3314115
+Netherlands: Milheeze,http://www.wikidata.org/entity/Q3314115
Nepal,http://www.wikidata.org/entity/Q837
New Zealand,http://www.wikidata.org/entity/Q664
Nicaragua,http://www.wikidata.org/entity/Q811
@@ -269,10 +277,14 @@ USA: AK,http://www.wikidata.org/entity/Q797
USA: AL,http://www.wikidata.org/entity/Q173
USA: AR,http://www.wikidata.org/entity/Q1612
USA: AZ,http://www.wikidata.org/entity/Q816
+USA: Arizona,http://www.wikidata.org/entity/Q816
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: CO,http://www.wikidata.org/entity/Q1261
USA: CT,http://www.wikidata.org/entity/Q779
+USA: Connecticut,http://www.wikidata.org/entity/Q779
USA: DC,http://www.wikidata.org/entity/Q3551781
USA: DE,http://www.wikidata.org/entity/Q1393
USA: FL,http://www.wikidata.org/entity/Q812
@@ -287,7 +299,7 @@ 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: New Orleans, LA",https://www.wikidata.org/wiki/Q34404
+"USA: New Orleans, LA",http://www.wikidata.org/entity/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
@@ -295,6 +307,8 @@ USA: ME,http://www.wikidata.org/entity/Q724
USA: MI,http://www.wikidata.org/entity/Q1166
USA: Michigan,http://www.wikidata.org/entity/Q1166
USA: MN,http://www.wikidata.org/entity/Q1527
+USA:Minnesota,http://www.wikidata.org/entity/Q1527
+USA: Minnesota,http://www.wikidata.org/entity/Q1527
USA: MO,http://www.wikidata.org/entity/Q1581
USA: MS,http://www.wikidata.org/entity/Q1494
USA: MT,http://www.wikidata.org/entity/Q1212
@@ -323,8 +337,10 @@ USA: TX,http://www.wikidata.org/entity/Q1439
USA: UT,http://www.wikidata.org/entity/Q829
USA: VA,http://www.wikidata.org/entity/Q1370
USA: Virginia,http://www.wikidata.org/entity/Q1370
+USA:Virginia,http://www.wikidata.org/entity/Q1370
USA: VT,http://www.wikidata.org/entity/Q16551
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: WV,http://www.wikidata.org/entity/Q1371
diff --git a/scripts/dict_ontology_standardization/ncbi_host_species.csv b/scripts/dict_ontology_standardization/ncbi_host_species.csv
index 0d2120c..102d458 100644
--- a/scripts/dict_ontology_standardization/ncbi_host_species.csv
+++ b/scripts/dict_ontology_standardization/ncbi_host_species.csv
@@ -1,4 +1,6 @@
Homo sapiens,http://purl.obolibrary.org/obo/NCBITaxon_9606
+human,http://purl.obolibrary.org/obo/NCBITaxon_9606
+Human,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
diff --git a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv
index 49cb6b7..110e90b 100644
--- a/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv
+++ b/scripts/dict_ontology_standardization/ncbi_sequencing_technology.csv
@@ -1,6 +1,13 @@
Illumian NextSeq 500,http://www.ebi.ac.uk/efo/EFO_0009173
Illumina NextSeq 500,http://www.ebi.ac.uk/efo/EFO_0009173
NextSeq500,http://www.ebi.ac.uk/efo/EFO_0009173
+NextSeq 500,http://www.ebi.ac.uk/efo/EFO_0009173
+Illumian NextSeq 550,http://www.ebi.ac.uk/efo/EFO_0008566
+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 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
diff --git a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
index 18b986c..0fa2219 100644
--- a/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
+++ b/scripts/dict_ontology_standardization/ncbi_speciesman_source.csv
@@ -14,6 +14,7 @@ oropharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155835
throat swab,http://purl.obolibrary.org/obo/NCIT_C155835
oro-pharyngeal,http://purl.obolibrary.org/obo/NCIT_C155835
Oropharyngal,http://purl.obolibrary.org/obo/NCIT_C155835
+oralpharyngeal,http://purl.obolibrary.org/obo/NCIT_C155835
Oral-pharyngeal,http://purl.obolibrary.org/obo/NCIT_C155835
Oro-pharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155835
Oropharyngeal swab,http://purl.obolibrary.org/obo/NCIT_C155835
diff --git a/scripts/docker/Dockerfile b/scripts/docker/Dockerfile
index 5bd38dd..9fb33d5 100644
--- a/scripts/docker/Dockerfile
+++ b/scripts/docker/Dockerfile
@@ -4,7 +4,7 @@ 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 \
- libssl-dev && \
+ libssl-dev libmagic-dev python3-magic && \
apt-get clean
-RUN pip3 install bh20-seq-uploader \ No newline at end of file
+RUN pip3 install bh20-seq-uploader
diff --git a/workflows/fastq2fasta/bam2fasta.cwl b/workflows/fastq2fasta/bam2fasta.cwl
index efe580f..dd4020b 100644
--- a/workflows/fastq2fasta/bam2fasta.cwl
+++ b/workflows/fastq2fasta/bam2fasta.cwl
@@ -15,6 +15,7 @@ inputs:
threads:
type: int
default: 4
+ sample_id: string
outputs:
out_fasta:
@@ -61,5 +62,6 @@ steps:
in:
ref_fasta: fasta
vcf: bcftools_index_after_qc/indexed
+ sample_id: sample_id
out: [out_fasta]
run: bcftools-consensus.cwl
diff --git a/workflows/fastq2fasta/bcftools-consensus.cwl b/workflows/fastq2fasta/bcftools-consensus.cwl
index c111792..dffdbe3 100644
--- a/workflows/fastq2fasta/bcftools-consensus.cwl
+++ b/workflows/fastq2fasta/bcftools-consensus.cwl
@@ -4,20 +4,27 @@ cwlVersion: v1.1
hints:
DockerRequirement:
dockerPull: "quay.io/biocontainers/bcftools:1.10.2--hd2cd319_0"
+ ShellCommandRequirement: {}
baseCommand: bcftools
arguments:
- consensus
- - -i'QUAL > 1 && GT="A"'
+ - -i
+ - 'QUAL > 1 && GT="a"'
- -Hla
- -f
- $(inputs.ref_fasta)
- $(inputs.vcf)
+ - {shellQuote: false, valueFrom: "|"}
+ - sed
+ - "s/^>.*/>$(inputs.sample_id)/g"
inputs:
- id: ref_fasta
type: File
- id: vcf
type: File
secondaryFiles: [.csi]
+ - id: sample_id
+ type: string
outputs:
- id: out_fasta
type: stdout
diff --git a/workflows/fastq2fasta/bcftools-view-qc.cwl b/workflows/fastq2fasta/bcftools-view-qc.cwl
index 477c596..336f455 100644
--- a/workflows/fastq2fasta/bcftools-view-qc.cwl
+++ b/workflows/fastq2fasta/bcftools-view-qc.cwl
@@ -8,7 +8,7 @@ baseCommand: bcftools
arguments:
- view
- -i
- - 'QUAL>1 && (GT="AA" || GT="Aa")'
+ - 'QUAL > 1 && GT="a"'
- -Oz
- --threads=$(inputs.threads)
- $(inputs.bcf)
diff --git a/workflows/fastq2fasta/fastq2fasta.cwl b/workflows/fastq2fasta/fastq2fasta.cwl
index 0cf5c48..d529d99 100644
--- a/workflows/fastq2fasta/fastq2fasta.cwl
+++ b/workflows/fastq2fasta/fastq2fasta.cwl
@@ -22,6 +22,7 @@ inputs:
type: int
default: 4
metadata: File?
+ sample_id: string
outputs:
out_fasta:
@@ -57,5 +58,6 @@ steps:
bam: samtools-sort/sorted_bam
fasta: ref_fasta
threads: threads
+ sample_id: sample_id
out: [out_fasta]
run: bam2fasta.cwl
generated by cgit v1.2.3 (git 2.44.0) at 2024-05-09 15:59:53 +0000