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authorAdam Novak2020-04-09 15:57:37 -0700
committerAdam Novak2020-04-09 15:58:56 -0700
commitd9a24cfb81a028fcd901abd08fc02b9140d5e78b (patch)
treeb08ac8d559a263381703ce14c06e144e6f48912c
parent2cd6623aa0ddfe4e42b2d434e0523773bb3536ef (diff)
parentb1039ff369ee88770e42d1bbbdc402b1181c2aa5 (diff)
downloadbh20-seq-resource-d9a24cfb81a028fcd901abd08fc02b9140d5e78b.tar.gz
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bh20-seq-resource-d9a24cfb81a028fcd901abd08fc02b9140d5e78b.zip
Merge remote-tracking branch 'upstream/master' into add-web-ui
-rw-r--r--README.md19
-rw-r--r--bh20seqanalyzer/main.py148
-rw-r--r--bh20sequploader/bh20seq-schema.yml89
-rw-r--r--bh20sequploader/main.py19
-rw-r--r--bh20sequploader/qc_metadata.py6
-rw-r--r--doc/DEVELOPMENT.md7
-rw-r--r--doc/INSTALL.md31
-rw-r--r--example/metadata.yaml49
-rw-r--r--example/minimal_example.yaml14
-rw-r--r--paper/paper.bib0
-rw-r--r--paper/paper.md110
11 files changed, 404 insertions, 88 deletions
diff --git a/README.md b/README.md
index 4667310..960472e 100644
--- a/README.md
+++ b/README.md
@@ -122,19 +122,7 @@ It should print some instructions about how to use the uploader.
## Installation with GNU Guix
-Another way to install this tool is inside a [GNU Guix Environment](https://guix.gnu.org/manual/en/html_node/Invoking-guix-environment.html), which can handle installing dependencies for you even when you don't have root access on an Ubuntu system.
-
-1. **Set up and enter a container with the necessary dependencies.** After installing Guix as `~/opt/guix/bin/guix`, run:
-
-```sh
-~/opt/guix/bin/guix environment -C guix --ad-hoc git python openssl python-pycurl nss-certs
-```
-
-2. **Install the tool.** From there you can follow the [user installation instructions](#installation-with-pip3---user). In brief:
-
-```sh
-pip3 install --user git+https://github.com/arvados/bh20-seq-resource.git@master
-```
+For running/developing the uploader with GNU Guix see [INSTALL.md](./doc/INSTALL.md)
# Usage
@@ -148,7 +136,7 @@ bh20-seq-uploader example/sequence.fasta example/metadata.json
All these uploaded sequences are being fed into a workflow to generate a [pangenome](https://academic.oup.com/bib/article/19/1/118/2566735) for the virus. You can replicate this workflow yourself.
-Get your SARS-CoV-2 sequences from GenBank in `seqs.fa`, and then run:
+An example is to get your SARS-CoV-2 sequences from GenBank in `seqs.fa`, and then run a series of commands
```sh
minimap2 -cx asm20 -X seqs.fa seqs.fa >seqs.paf
@@ -157,6 +145,9 @@ odgi build -g seqs.gfa -s -o seqs.odgi
odgi viz -i seqs.odgi -o seqs.png -x 4000 -y 500 -R -P 5
```
+Here we convert such a pipeline into the Common Workflow Language (CWL) and
+sources can be found [here](https://github.com/hpobio-lab/viral-analysis/tree/master/cwl/pangenome-generate).
+
For more information on building pangenome models, [see this wiki page](https://github.com/virtual-biohackathons/covid-19-bh20/wiki/Pangenome#pangenome-model-from-available-genomes).
# Web Interface
diff --git a/bh20seqanalyzer/main.py b/bh20seqanalyzer/main.py
index 78e32c9..2030c1e 100644
--- a/bh20seqanalyzer/main.py
+++ b/bh20seqanalyzer/main.py
@@ -13,21 +13,30 @@ logging.basicConfig(format="[%(asctime)s] %(levelname)s %(message)s", datefmt="%
level=logging.INFO)
logging.getLogger("googleapiclient.discovery").setLevel(logging.WARN)
-def validate_upload(api, collection, validated_project):
+def validate_upload(api, collection, validated_project,
+ fastq_project, fastq_workflow_uuid):
col = arvados.collection.Collection(collection["uuid"])
# validate the collection here. Check metadata, etc.
valid = True
- if "sequence.fasta" not in col:
- valid = False
- logging.warn("Upload '%s' missing sequence.fasta", collection["name"])
if "metadata.yaml" not in col:
logging.warn("Upload '%s' missing metadata.yaml", collection["name"])
valid = False
else:
metadata_content = ruamel.yaml.round_trip_load(col.open("metadata.yaml"))
- valid = qc_metadata(metadata_content) and valid
+ #valid = qc_metadata(metadata_content) and valid
+ if not valid:
+ logging.warn("Failed metadata qc")
+
+ if valid:
+ if "sequence.fasta" not in col:
+ if "reads.fastq" in col:
+ start_fastq_to_fasta(api, collection, fastq_project, fastq_workflow_uuid)
+ return False
+ else:
+ valid = False
+ logging.warn("Upload '%s' missing sequence.fasta", collection["name"])
dup = api.collections().list(filters=[["owner_uuid", "=", validated_project],
["portable_data_hash", "=", col.portable_data_hash()]]).execute()
@@ -39,7 +48,9 @@ def validate_upload(api, collection, validated_project):
if valid:
logging.info("Added '%s' to validated sequences" % collection["name"])
# Move it to the "validated" project to be included in the next analysis
- api.collections().update(uuid=collection["uuid"], body={"owner_uuid": validated_project}).execute()
+ api.collections().update(uuid=collection["uuid"], body={
+ "owner_uuid": validated_project,
+ "name": "%s (%s)" % (collection["name"], time.asctime(time.gmtime()))}).execute()
else:
# It is invalid, delete it.
logging.warn("Deleting '%s'" % collection["name"])
@@ -47,28 +58,15 @@ def validate_upload(api, collection, validated_project):
return valid
-def start_analysis(api,
- analysis_project,
- workflow_uuid,
- validated_project):
+def run_workflow(api, parent_project, workflow_uuid, name, inputobj):
project = api.groups().create(body={
"group_class": "project",
- "name": "Pangenome analysis",
- "owner_uuid": analysis_project,
+ "name": name,
+ "owner_uuid": parent_project,
}, ensure_unique_name=True).execute()
- validated = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", validated_project]])
-
with tempfile.NamedTemporaryFile() as tmp:
- inputobj = {
- "inputReads": []
- }
- for v in validated:
- inputobj["inputReads"].append({
- "class": "File",
- "location": "keep:%s/sequence.fasta" % v["portable_data_hash"]
- })
tmp.write(json.dumps(inputobj, indent=2).encode('utf-8'))
tmp.flush()
cmd = ["arvados-cwl-runner",
@@ -83,32 +81,102 @@ def start_analysis(api,
if comp.returncode != 0:
logging.error(comp.stderr.decode('utf-8'))
+ return project
+
+
+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"]
+ },
+ "metadata": {
+ "class": "File",
+ "location": "keep:%s/metadata.yaml" % collection["portable_data_hash"]
+ },
+ "ref_fasta": {
+ "class": "File",
+ "location": "keep:ffef6a3b77e5e04f8f62a7b6f67264d1+556/SARS-CoV2-NC_045512.2.fasta"
+ }
+ })
+ api.collections().update(uuid=collection["uuid"],
+ body={"owner_uuid": newproject["uuid"]}).execute()
+
+def start_pangenome_analysis(api,
+ analysis_project,
+ pangenome_workflow_uuid,
+ validated_project):
+ validated = arvados.util.list_all(api.collections().list, filters=[["owner_uuid", "=", validated_project]])
+ inputobj = {
+ "inputReads": [],
+ "metadata": [],
+ "subjects": []
+ }
+ for v in validated:
+ inputobj["inputReads"].append({
+ "class": "File",
+ "location": "keep:%s/sequence.fasta" % v["portable_data_hash"]
+ })
+ inputobj["metadata"].append({
+ "class": "File",
+ "location": "keep:%s/metadata.yaml" % v["portable_data_hash"]
+ })
+ inputobj["subjects"].append("keep:%s/sequence.fasta" % v["portable_data_hash"])
+ run_workflow(api, analysis_project, pangenome_workflow_uuid, "Pangenome analysis", inputobj)
+
+
+def get_workflow_output_from_project(api, uuid):
+ cr = api.container_requests().list(filters=[['owner_uuid', '=', uuid],
+ ["requesting_container_uuid", "=", None]]).execute()
+ if cr["items"] and cr["items"][0]["output_uuid"]:
+ return cr["items"][0]
+ else:
+ return None
+
def copy_most_recent_result(api, analysis_project, latest_result_uuid):
most_recent_analysis = api.groups().list(filters=[['owner_uuid', '=', analysis_project]],
order="created_at desc", limit=1).execute()
for m in most_recent_analysis["items"]:
- cr = api.container_requests().list(filters=[['owner_uuid', '=', m["uuid"]],
- ["requesting_container_uuid", "=", None]]).execute()
- if cr["items"] and cr["items"][0]["output_uuid"]:
- wf = cr["items"][0]
+ wf = get_workflow_output_from_project(api, m["uuid"])
+ if wf:
src = api.collections().get(uuid=wf["output_uuid"]).execute()
dst = api.collections().get(uuid=latest_result_uuid).execute()
if src["portable_data_hash"] != dst["portable_data_hash"]:
logging.info("Copying latest result from '%s' to %s", m["name"], latest_result_uuid)
api.collections().update(uuid=latest_result_uuid,
body={"manifest_text": src["manifest_text"],
- "description": "latest result from %s %s" % (m["name"], wf["uuid"])}).execute()
+ "description": "Result from %s %s" % (m["name"], wf["uuid"])}).execute()
break
+def move_fastq_to_fasta_results(api, analysis_project, uploader_project):
+ projects = api.groups().list(filters=[['owner_uuid', '=', analysis_project],
+ ["properties.moved_output", "!=", True]],
+ order="created_at desc",).execute()
+ for p in projects["items"]:
+ wf = get_workflow_output_from_project(api, p["uuid"])
+ if wf:
+ logging.info("Moving completed fastq2fasta result %s back to uploader project", wf["output_uuid"])
+ api.collections().update(uuid=wf["output_uuid"],
+ body={"owner_uuid": uploader_project}).execute()
+ p["properties"]["moved_output"] = True
+ api.groups().update(uuid=p["uuid"], body={"properties": p["properties"]}).execute()
+
+
def main():
parser = argparse.ArgumentParser(description='Analyze collections uploaded to a project')
parser.add_argument('--uploader-project', type=str, default='lugli-j7d0g-n5clictpuvwk8aa', help='')
- parser.add_argument('--analysis-project', type=str, default='lugli-j7d0g-y4k4uswcqi3ku56', help='')
+ parser.add_argument('--pangenome-analysis-project', type=str, default='lugli-j7d0g-y4k4uswcqi3ku56', help='')
+ parser.add_argument('--fastq-project', type=str, default='lugli-j7d0g-xcjxp4oox2u1w8u', help='')
parser.add_argument('--validated-project', type=str, default='lugli-j7d0g-5ct8p1i1wrgyjvp', help='')
- parser.add_argument('--workflow-uuid', type=str, default='lugli-7fd4e-mqfu9y3ofnpnho1', help='')
- parser.add_argument('--latest-result-uuid', type=str, default='lugli-4zz18-z513nlpqm03hpca', help='')
+
+ parser.add_argument('--pangenome-workflow-uuid', type=str, default='lugli-7fd4e-mqfu9y3ofnpnho1', help='')
+ parser.add_argument('--fastq-workflow-uuid', type=str, default='lugli-7fd4e-2zp9q4jo5xpif9y', help='')
+
+ parser.add_argument('--latest-result-collection', type=str, default='lugli-4zz18-z513nlpqm03hpca', help='')
args = parser.parse_args()
api = arvados.api()
@@ -116,16 +184,24 @@ def main():
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()
at_least_one_new_valid_seq = False
for c in new_collections["items"]:
- at_least_one_new_valid_seq = validate_upload(api, c, args.validated_project) or at_least_one_new_valid_seq
+ 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:
- start_analysis(api, args.analysis_project,
- args.workflow_uuid,
- args.validated_project)
+ start_pangenome_analysis(api,
+ args.pangenome_analysis_project,
+ args.pangenome_workflow_uuid,
+ args.validated_project)
- copy_most_recent_result(api, args.analysis_project, args.latest_result_uuid)
+ copy_most_recent_result(api,
+ args.pangenome_analysis_project,
+ args.latest_result_collection)
- time.sleep(10)
+ time.sleep(15)
diff --git a/bh20sequploader/bh20seq-schema.yml b/bh20sequploader/bh20seq-schema.yml
index 6e0973a..5c962d1 100644
--- a/bh20sequploader/bh20seq-schema.yml
+++ b/bh20sequploader/bh20seq-schema.yml
@@ -1,36 +1,89 @@
+$base: http://biohackathon.org/bh20-seq-schema
+$namespaces:
+ sch: https://schema.org/
+ efo: http://www.ebi.ac.uk/efo/
+ obo: http://purl.obolibrary.org/obo/
$graph:
-- name: sampleInformationSchema
+- name: hostSchema
type: record
fields:
- location: string
- host: string
- sequenceTechnology: string
- assemblyMethod: string
+ host_species:
+ type: string
+ jsonldPredicate:
+ _id: http://www.ebi.ac.uk/efo/EFO_0000532
+ host_id: string
+ host_common_name: string?
+ host_sex: string?
+ host_age: int?
+ host_age_unit: string?
+ host_health_status: string?
+ host_treatment:
+ type: string?
+ jsonldPredicate:
+ _id: http://www.ebi.ac.uk/efo/EFO_0000727
+ additional_host_information: string?
-- name: InstituteInformationSchema
+- name: sampleSchema
type: record
fields:
- OriginatingLab: string
- SubmittingLab: string
+ collector_name: string
+ collecting_institution: string
+ specimen_source: string?
+ collection_date: string?
+ collection_location:
+ type: string?
+ jsonldPredicate:
+ _id: https://schema.org/fromLocation
+ sample_storage_conditions: string?
+ additional_collection_information: string?
-- name: SubmitterInformationSchema
+- name: virusSchema
type: record
fields:
- Submitter: string
- submissionDate: string
+ virus_species: string?
+ virus_strain: string?
-- name: VirusDetailSchema
+- name: technologySchema
type: record
fields:
- VirusName: string
- AccessionId: string
+ sample_sequencing_technology:
+ type: string
+ jsonldPredicate:
+ _id: http://www.ebi.ac.uk/efo/EFO_0000532
+ sequence_assembly_method:
+ type: string?
+ jsonldPredicate:
+ _id: http://www.ebi.ac.uk/efo/EFO_0002699
+ sequencing_coverage:
+ type: string?
+ jsonldPredicate:
+ _id: http://purl.obolibrary.org/obo/FLU_0000848
+
+- name: submitterSchema
+ type: record
+ fields:
+ submitter_name: string
+ submitter_address: string?
+ originating_lab: string
+ lab_address: string?
+ provider_sample_id: string?
+ submitter_sample_id: string?
+ authors: string?
+ submitter_id: string?
- name: MainSchema
type: record
documentRoot: true
fields:
- sampleInformation: sampleInformationSchema
- InstituteInformation: InstituteInformationSchema
- SubmitterInformation: SubmitterInformationSchema
- VirusDetail: VirusDetailSchema
+ host: hostSchema
+ sample: sampleSchema
+ virus: virusSchema?
+ technology: technologySchema
+ submitter: submitterSchema
+ sequencefile:
+ doc: The subject (eg the fasta/fastq file) that this metadata describes
+ type: string?
+ jsonldPredicate:
+ _id: "@id"
+ _type: "@id"
diff --git a/bh20sequploader/main.py b/bh20sequploader/main.py
index d3ebc0c..bf74ea5 100644
--- a/bh20sequploader/main.py
+++ b/bh20sequploader/main.py
@@ -6,6 +6,7 @@ import json
import urllib.request
import socket
import getpass
+import qc_metadata
ARVADOS_API_HOST='lugli.arvadosapi.com'
ARVADOS_API_TOKEN='2fbebpmbo3rw3x05ueu2i6nx70zhrsb1p22ycu3ry34m4x4462'
@@ -19,18 +20,26 @@ def main():
api = arvados.api(host=ARVADOS_API_HOST, token=ARVADOS_API_TOKEN, insecure=True)
+ if not qc_metadata(args.metadata.name):
+ print("Failed metadata qc")
+ exit(1)
+
col = arvados.collection.Collection(api_client=api)
- print("Reading FASTA")
- with col.open("sequence.fasta", "w") as f:
+ if args.sequence.name.endswith("fasta") or args.sequence.name.endswith("fa"):
+ target = "sequence.fasta"
+ elif args.sequence.name.endswith("fastq") or args.sequence.name.endswith("fq"):
+ target = "reads.fastq"
+
+ with col.open(target, "w") as f:
r = args.sequence.read(65536)
print(r[0:20])
while r:
f.write(r)
r = args.sequence.read(65536)
- print("Reading JSONLD")
- with col.open("metadata.jsonld", "w") as f:
+ print("Reading metadata")
+ with col.open("metadata.yaml", "w") as f:
r = args.metadata.read(65536)
print(r[0:20])
while r:
@@ -49,5 +58,7 @@ def main():
(properties['upload_user'], properties['upload_ip']),
properties=properties, ensure_unique_name=True)
+ print("Done")
+
if __name__ == "__main__":
main()
diff --git a/bh20sequploader/qc_metadata.py b/bh20sequploader/qc_metadata.py
index 78b31b2..ebe4dfc 100644
--- a/bh20sequploader/qc_metadata.py
+++ b/bh20sequploader/qc_metadata.py
@@ -1,6 +1,7 @@
import schema_salad.schema
import logging
import pkg_resources
+import logging
def qc_metadata(metadatafile):
schema_resource = pkg_resources.resource_stream(__name__, "bh20seq-schema.yml")
@@ -17,5 +18,6 @@ def qc_metadata(metadatafile):
try:
doc, metadata = schema_salad.schema.load_and_validate(document_loader, avsc_names, metadatafile, True)
return True
- except:
- return False
+ except Exception as e:
+ logging.warn(e)
+ return False
diff --git a/doc/DEVELOPMENT.md b/doc/DEVELOPMENT.md
new file mode 100644
index 0000000..98d8de4
--- /dev/null
+++ b/doc/DEVELOPMENT.md
@@ -0,0 +1,7 @@
+# Development
+
+## Upload resume
+
+When data files get large we may want to implement resume,
+like put does. See
+[/sdk/python/arvados/commands/put.py](https://dev.arvados.org/projects/arvados/repository/revisions/master/entry/sdk/python/arvados/commands/put.py)
diff --git a/doc/INSTALL.md b/doc/INSTALL.md
new file mode 100644
index 0000000..c5c486c
--- /dev/null
+++ b/doc/INSTALL.md
@@ -0,0 +1,31 @@
+# INSTALLATION
+
+Other options for running this tool.
+
+## GNU Guix
+
+Another way to install this tool is inside a [GNU Guix Environment](https://guix.gnu.org/manual/en/html_node/Invoking-guix-environment.html), which can handle installing dependencies for you even when you don't have root access on an Ubuntu system.
+
+1. **Set up and enter a container with the necessary dependencies.** After installing Guix as `~/opt/guix/bin/guix`, run:
+
+```sh
+~/opt/guix/bin/guix environment -C guix --ad-hoc git python openssl python-pycurl nss-certs
+```
+
+2. **Install the tool.** From there you can follow the [user installation instructions](#installation-with-pip3---user). In brief:
+
+```sh
+pip3 install --user schema-salad arvados-python-client
+```
+
+Pip installed the following modules
+
+```
+arvados-python-client-2.0.1 ciso8601-2.1.3 future-0.18.2 google-api-python-client-1.6.7 httplib2-0.17.1 oauth2client-4.1.3 pyasn1-0.4.8 pyasn1-modules-0.2.8 rsa-4.0 ruamel.yaml-0.15.77 six-1.14.0 uritemplate-3.0.1 ws4py-0.5.1
+```
+
+3. Run the tool directly with
+
+```sh
+~/opt/guix/bin/guix environment guix --ad-hoc git python openssl python-pycurl nss-certs -- python3 bh20sequploader/main.py
+```
diff --git a/example/metadata.yaml b/example/metadata.yaml
index 587d0be..41ff93e 100644
--- a/example/metadata.yaml
+++ b/example/metadata.yaml
@@ -1,17 +1,38 @@
-sampleInformation:
- location: "USA"
- host : "Homo Sapiens"
- sequenceTechnology: "Sanger"
- assemblyMethod: "CLC Genomics"
+host:
+ host_id: XX1
+ host_species: string
+ host_common_name: string
+ host_sex: string
+ host_age: 20
+ host_age_unit: string
+ host_health_status: string
+ host_treatment: string
+ additional_host_information: string
-InstituteInformation:
- OriginatingLab: "Erik's kitchen"
- SubmittingLab: "National Institute for Viral Disease Control and Prevention, China CDC"
+sample:
+ collector_name: XXX
+ collecting_institution: XXX
+ specimen_source: XXX
+ collection_date: XXX
+ collection_location: XXX
+ sample_storage_conditions: XXX
+ additional_collection_information: XXX
-SubmitterInformation:
- Submitter: "National Institute for Viral Disease Control and Prevention, China CDC"
- submissionDate: "04-04-2020"
+virus:
+ virus_species: XX
+ virus_strain: XX
-VirusDetail:
- VirusName: "hCoV-19/USA/identifer/2020"
- AccessionId: "EPI_ISL_Random"
+technology:
+ sample_sequencing_technology: XX
+ sequence_assembly_method: XX
+ sequencing_coverage: 70x
+
+submitter:
+ submitter_name: tester
+ submitter_address: testerAdd
+ originating_lab: testLab
+ lab_address: labAdd
+ provider_sample_id: string
+ submitter_sample_id: string
+ authors: testAuthor
+ submitter_id: X12
diff --git a/example/minimal_example.yaml b/example/minimal_example.yaml
new file mode 100644
index 0000000..201b080
--- /dev/null
+++ b/example/minimal_example.yaml
@@ -0,0 +1,14 @@
+host:
+ host_id: XX
+ host_species: string
+
+sample:
+ collector_name: XXX
+ collecting_institution: XXX
+
+technology:
+ sample_sequencing_technology: XX
+
+submitter:
+ submitter_name: tester
+ originating_lab: testLab \ No newline at end of file
diff --git a/paper/paper.bib b/paper/paper.bib
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/paper/paper.bib
diff --git a/paper/paper.md b/paper/paper.md
new file mode 100644
index 0000000..caa9903
--- /dev/null
+++ b/paper/paper.md
@@ -0,0 +1,110 @@
+---
+title: 'Public Sequence Resource for COVID-19'
+tags:
+ - Sequencing
+ - COVID
+authors:
+ - name: Pjotr Prins
+ orcid: 0000-0002-8021-9162
+ affiliation: 1
+ - name: Peter Amstutz
+ orcid: 0000
+ affiliation: 2
+ - name: Tazro Ohta
+ orcid: 0000
+ affiliation: 3
+ - name: Thomas Liener
+ orcid: 0000
+ affiliation: 4
+ - name: Erik Garrison
+ orcid: 0000
+ affiliation: 5
+ - name: Michael Crusoe
+ orcid: 0000
+ affiliation: 6
+ - name: Rutger Vos
+ orcid: 0000
+ affiliation: 7
+ - Michael Heuer
+ orcid: 0000
+ affiliation: 8
+
+affiliations:
+ - name: Department of Genetics, Genomics and Informatics, The University of Tennessee Health Science Center, Memphis, TN, USA.
+ index: 1
+ - name: Curii, Boston, USA
+ index: 2
+date: 11 April 2020
+bibliography: paper.bib
+---
+
+<!--
+
+The paper.md, bibtex and figure file can be found in this repo:
+
+ https://github.com/arvados/bh20-seq-resource
+
+To modify, please clone the repo. You can generate PDF of the paper by
+pasting above link (or yours) with
+
+ https://github.com/biohackrxiv/bhxiv-gen-pdf
+
+-->
+
+# Introduction
+
+As part of the one week COVID-19 Biohackathion 2020, we formed a
+working group on creating a public sequence resource for Corona virus.
+
+
+<!--
+
+ RESULTS!
+
+ For each section below
+
+ State the problem you worked on
+ Give the state-of-the art/plan
+ Describe what you have done/results starting with The working group created...
+ Write a conclusion
+ Write up any future work
+
+-->
+
+## Cloud computing backend
+
+Peter, Pjotr, MichaelC
+
+## A command-line sequence uploader
+
+Peter, Pjotr
+
+## Metadata uploader
+
+With Thomas
+
+## FASTA to GFA workflow
+
+Michael Heuer
+
+## BAM to GFA workflow
+
+Tazro & Erik
+
+## Phylogeny app
+
+With Rutger
+
+## RDF app
+
+Jerven?
+
+## EBI app
+
+?
+
+# Discussion
+
+Future work...
+
+# References