+In this document we explain how to upload data into COVID-19 PubSeq.
+This can happen through a web page, or through a command line
+script. We'll also show how to parametrize uploads by using templates.
+The procedure is much easier than with other repositories and can be
+fully automated. Once uploaded you can use our export API to prepare
+for other repositories.
+
+
+
-
-
1 Uploading Data
-
+
+
2 Uploading data
+
The COVID-19 PubSeq allows you to upload your SARS-Cov-2 strains to a
public resource for global comparisons. A recompute of the pangenome
@@ -278,9 +292,9 @@ gets triggered on upload. Read the ABOUT page for more inf
-
-
2 Step 1: Upload sequence
-
+
+
3 Step 1: Upload sequence
+
To upload a sequence in the web upload page hit the browse button and
select the FASTA file on your local hard disk.
@@ -307,9 +321,9 @@ an improved pangenome.
-
-
3 Step 2: Add metadata
-
+
+
4 Step 2: Add metadata
+
The web upload page contains fields for adding metadata. Metadata is
not only important for attribution, is also important for
@@ -334,13 +348,13 @@ the web form. Here we add some extra information.
-
-
3.1 Obligatory fields
-
+
+
4.1 Obligatory fields
+
-
-
3.1.1 Sample ID (sample_id)
-
+
+
4.1.1 Sample ID (sample_id)
+
This is a string field that defines a unique sample identifier by the
submitter. In addition to sample_id we also have host_id,
@@ -357,18 +371,18 @@ Here we add the GenBank ID MT536190.1.
-
-
3.1.2 Collection date
-
+
+
4.1.2 Collection date
+
Estimated collection date. The GenBank page says April 6, 2020.
GenBank entry says Illumina, so we can fill that in
-
-
3.1.5 Authors
-
+
+
4.1.5 Authors
+
GenBank entry says 'Lamers,S., Nolan,D.J., Rose,R., Cross,S., Moraga
Amador,D., Yang,T., Caruso,L., Navia,W., Von Borstel,L., Hui Zhou,X.,
@@ -397,17 +411,17 @@ Freehan,A. and Garcia-Diaz,J.', so we can fill that in.
-
-
3.2 Optional fields
-
+
+
4.2 Optional fields
+
All other fields are optional. But let's see what we can add.
-
-
3.2.1 Host information
-
+
+
4.2.1 Host information
+
Sadly, not much is known about the host from GenBank. A little
sleuthing renders an interesting paper by some of the authors titled
@@ -420,27 +434,27 @@ did to the person and what the person was like (say age group).
Once you have the sequence and the metadata together, hit
the 'Add to Pangenome' button. The data will be checked,
@@ -470,9 +484,9 @@ submitted and the workflows should kick in!
-
-
4.1 Trouble shooting
-
+
+
5.1 Trouble shooting
+
We got an error saying: {"stem": "http://www.wikidata.org/entity/",…
which means that our location field was not formed correctly! After
@@ -485,9 +499,9 @@ submit button.
-
-
5 Step 4: Check output
-
+
+
6 Step 4: Check output
+
The current pipeline takes 5.5 hours to complete! Once it completes
the updated data can be checked on the DOWNLOAD page. After completion
@@ -497,9 +511,9 @@ in.
-
-
6 Bulk sequence uploader
-
+
+
7 Bulk sequence uploader
+
Above steps require a manual upload of one sequence with metadata.
What if you have a number of sequences you want to upload in bulk?
@@ -510,6 +524,39 @@ the web form and gets validated from the same
+
+a more elaborate example (note most fields are optional) may look like
+
+
id: placeholder
@@ -559,11 +606,20 @@ submitter:
additional_submitter_information: Optional free text field for additional information
+
+
+more metadata is yummy. Yummydata is useful to a wider community. Note
+that many of the terms in above example are URIs, such as
+host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606. We use
+web ontologies for these to make the data less ambiguous and more
+FAIR. Check out the option fields as defined in the schema. If it is not listed
+a little bit of web searching may be required or contact us.
+
-
-
6.1 Run the uploader (CLI)
-
+
+
7.1 Run the uploader (CLI)
+
Installing with pip you should be
able to run
@@ -574,7 +630,6 @@ bh20sequploader sequence.fasta metadata.yaml
-
Alternatively the script can be installed from github. Run on the
command line
@@ -617,9 +672,9 @@ The web interface using this exact same script so it should just work
-
-
6.2 Example: uploading bulk GenBank sequences
-
+
+
7.2 Example: uploading bulk GenBank sequences
+
We also use above script to bulk upload GenBank sequences with a FASTA
and YAML extractor specific for GenBank. This means that the steps we
@@ -645,14 +700,15 @@ ls $dir_fasta_and_yaml/*.yaml |
-
-
6.3 Example: preparing metadata
-
+
+
7.3 Example: preparing metadata
+
-Usually, metadata are available in tabular format, like spreadsheets. As an example, we provide a script
-esr_samples.py to show you how to parse
-your metadata in YAML files ready for the upload. To execute the script, go in the ~bh20-seq-resource/scripts/esr_samples
-and execute
+Usually, metadata are available in a tabular format, such as
+spreadsheets. As an example, we provide a script esr_samples.py to
+show you how to parse your metadata in YAML files ready for the
+upload. To execute the script, go in the
+~bh20-seq-resource/scripts/esr_samples and execute
@@ -661,14 +717,27 @@ and execute
-You will find the YAML files in the `yaml` folder which will be created in the same directory.
+You will find the YAML files in the `yaml` folder which will be
+created in the same directory.
+
+
+
+In the example we use Python pandas to read the spreadsheet into a
+tabular structure. Next we use a template.yaml file that gets filled
+in by esr_samples.py so we get a metadata YAML file for each sample.
+
+
+
+Next run the earlier CLI uploader for each YAML and FASTA combination.
+It can't be much easier than this. For ESR we uploaded a batch of 600
+sequences this way. See example.
-Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp! Modified 2020-10-27 Tue 06:43.
+Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp! Modified 2020-11-05 Thu 07:27.
diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org
index fb68251..f3ba073 100644
--- a/doc/blog/using-covid-19-pubseq-part3.org
+++ b/doc/blog/using-covid-19-pubseq-part3.org
@@ -7,10 +7,19 @@
#+HTML_HEAD:
#+OPTIONS: ^:nil
+* Introduction
+
+In this document we explain how to upload data into COVID-19 PubSeq.
+This can happen through a web page, or through a command line
+script. We'll also show how to parametrize uploads by using templates.
+The procedure is much easier than with other repositories and can be
+fully automated. Once uploaded you can use our export API to prepare
+for other repositories.
* Table of Contents :TOC:noexport:
- - [[#uploading-data][Uploading Data]]
+ - [[#introduction][Introduction]]
+ - [[#uploading-data][Uploading data]]
- [[#step-1-upload-sequence][Step 1: Upload sequence]]
- [[#step-2-add-metadata][Step 2: Add metadata]]
- [[#obligatory-fields][Obligatory fields]]
@@ -23,7 +32,7 @@
- [[#example-uploading-bulk-genbank-sequences][Example: uploading bulk GenBank sequences]]
- [[#example-preparing-metadata][Example: preparing metadata]]
-* Uploading Data
+* Uploading data
The COVID-19 PubSeq allows you to upload your SARS-Cov-2 strains to a
public resource for global comparisons. A recompute of the pangenome
@@ -165,55 +174,90 @@ file an associated metadata in [[https://github.com/arvados/bh20-seq-resource/bl
the web form and gets validated from the same [[https://github.com/arvados/bh20-seq-resource/blob/master/bh20sequploader/bh20seq-schema.yml][schema]] looks. The YAML
that you need to create/generate for your samples looks like
+A minimal example of metadata looks like
+
+#+begin_src json
+ id: placeholder
+
+ license:
+ license_type: http://creativecommons.org/licenses/by/4.0/
+
+ host:
+ host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606
+
+ sample:
+ sample_id: XX
+ collection_date: "2020-01-01"
+ collection_location: http://www.wikidata.org/entity/Q148
+
+ virus:
+ virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049
+
+ technology:
+ sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632]
+
+ submitter:
+ authors: [John Doe]
+#+end_src
+
+a more elaborate example (note most fields are optional) may look like
+
#+begin_src json
-id: placeholder
-
-host:
- host_id: XX1
- host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606
- host_sex: http://purl.obolibrary.org/obo/PATO_0000384
- host_age: 20
- host_age_unit: http://purl.obolibrary.org/obo/UO_0000036
- host_health_status: http://purl.obolibrary.org/obo/NCIT_C25269
- host_treatment: Process in which the act is intended to modify or alter host status (Compounds)
- host_vaccination: [vaccines1,vaccine2]
- ethnicity: http://purl.obolibrary.org/obo/HANCESTRO_0010
- additional_host_information: Optional free text field for additional information
-
-sample:
- sample_id: Id of the sample as defined by the submitter
- collector_name: Name of the person that took the sample
- collecting_institution: Institute that was responsible of sampling
- specimen_source: [http://purl.obolibrary.org/obo/NCIT_C155831,http://purl.obolibrary.org/obo/NCIT_C155835]
- collection_date: "2020-01-01"
- collection_location: http://www.wikidata.org/entity/Q148
- sample_storage_conditions: frozen specimen
- source_database_accession: [http://identifiers.org/insdc/LC522350.1#sequence]
- additional_collection_information: Optional free text field for additional information
-
-virus:
- virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049
- virus_strain: SARS-CoV-2/human/CHN/HS_8/2020
-
-technology:
- sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0009173,http://www.ebi.ac.uk/efo/EFO_0009173]
- sequence_assembly_method: Protocol used for assembly
- sequencing_coverage: [70.0, 100.0]
- additional_technology_information: Optional free text field for additional information
-
-submitter:
- authors: [John Doe, Joe Boe, Jonny Oe]
- submitter_name: [John Doe]
- submitter_address: John Doe's address
- originating_lab: John Doe kitchen
- lab_address: John Doe's address
- provider_sample_id: XXX1
- submitter_sample_id: XXX2
- publication: PMID00001113
- submitter_orcid: [https://orcid.org/0000-0000-0000-0000,https://orcid.org/0000-0000-0000-0001]
- additional_submitter_information: Optional free text field for additional information
+ id: placeholder
+
+ host:
+ host_id: XX1
+ host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606
+ host_sex: http://purl.obolibrary.org/obo/PATO_0000384
+ host_age: 20
+ host_age_unit: http://purl.obolibrary.org/obo/UO_0000036
+ host_health_status: http://purl.obolibrary.org/obo/NCIT_C25269
+ host_treatment: Process in which the act is intended to modify or alter host status (Compounds)
+ host_vaccination: [vaccines1,vaccine2]
+ ethnicity: http://purl.obolibrary.org/obo/HANCESTRO_0010
+ additional_host_information: Optional free text field for additional information
+
+ sample:
+ sample_id: Id of the sample as defined by the submitter
+ collector_name: Name of the person that took the sample
+ collecting_institution: Institute that was responsible of sampling
+ specimen_source: [http://purl.obolibrary.org/obo/NCIT_C155831,http://purl.obolibrary.org/obo/NCIT_C155835]
+ collection_date: "2020-01-01"
+ collection_location: http://www.wikidata.org/entity/Q148
+ sample_storage_conditions: frozen specimen
+ source_database_accession: [http://identifiers.org/insdc/LC522350.1#sequence]
+ additional_collection_information: Optional free text field for additional information
+
+ virus:
+ virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049
+ virus_strain: SARS-CoV-2/human/CHN/HS_8/2020
+
+ technology:
+ sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0009173,http://www.ebi.ac.uk/efo/EFO_0009173]
+ sequence_assembly_method: Protocol used for assembly
+ sequencing_coverage: [70.0, 100.0]
+ additional_technology_information: Optional free text field for additional information
+
+ submitter:
+ authors: [John Doe, Joe Boe, Jonny Oe]
+ submitter_name: [John Doe]
+ submitter_address: John Doe's address
+ originating_lab: John Doe kitchen
+ lab_address: John Doe's address
+ provider_sample_id: XXX1
+ submitter_sample_id: XXX2
+ publication: PMID00001113
+ submitter_orcid: [https://orcid.org/0000-0000-0000-0000,https://orcid.org/0000-0000-0000-0001]
+ additional_submitter_information: Optional free text field for additional information
#+end_src
+more metadata is yummy when stored in RDF. [[https://yummydata.org/][Yummydata]] is useful to a wider community. Note
+that many of the terms in above example are URIs, such as
+host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606. We use
+web ontologies for these to make the data less ambiguous and more
+FAIR. Check out the option fields as defined in the schema. If it is not listed
+a little bit of web searching may be required or [[./contact][contact]] us.
+
** Run the uploader (CLI)
Installing with pip you should be
@@ -221,7 +265,6 @@ able to run
: bh20sequploader sequence.fasta metadata.yaml
-
Alternatively the script can be installed from [[https://github.com/arvados/bh20-seq-resource#installation][github]]. Run on the
command line
@@ -274,13 +317,23 @@ done
** Example: preparing metadata
-Usually, metadata are available in tabular format, like spreadsheets. As an example, we provide a script
-[[https://github.com/arvados/bh20-seq-resource/tree/master/scripts/esr_samples][esr_samples.py]] to show you how to parse
-your metadata in YAML files ready for the upload. To execute the script, go in the ~bh20-seq-resource/scripts/esr_samples
-and execute
+Usually, metadata are available in a tabular format, such as
+spreadsheets. As an example, we provide a script [[https://github.com/arvados/bh20-seq-resource/tree/master/scripts/esr_samples][esr_samples.py]] to
+show you how to parse your metadata in YAML files ready for the
+upload. To execute the script, go in the
+~bh20-seq-resource/scripts/esr_samples and execute
#+BEGIN_SRC sh
python3 esr_samples.py
#+END_SRC
-You will find the YAML files in the `yaml` folder which will be created in the same directory.
+You will find the YAML files in the `yaml` folder which will be
+created in the same directory.
+
+In the example we use Python pandas to read the spreadsheet into a
+tabular structure. Next we use a [[https://github.com/arvados/bh20-seq-resource/blob/master/scripts/esr_samples/template.yaml][template.yaml]] file that gets filled
+in by ~esr_samples.py~ so we get a metadata YAML file for each sample.
+
+Next run the earlier CLI uploader for each YAML and FASTA combination.
+It can't be much easier than this. For ESR we uploaded a batch of 600
+sequences this way writing a few lines of Python [[https://github.com/arvados/bh20-seq-resource/blob/master/scripts/esr_samples/esr_samples.py][code]]. See [[http://covid19.genenetwork.org/resource/20VR0995][example]].
--
cgit v1.2.3
From 43d7264dda8061a024befbc9ca0a89d7159b1e40 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Fri, 6 Nov 2020 09:52:32 +0000
Subject: UTHSC upload info
---
doc/blog/using-covid-19-pubseq-part3.org | 3 +-
scripts/uthsc_samples/.gitignore | 1 +
scripts/uthsc_samples/template.yaml | 35 ++++++++++++++++++++
scripts/uthsc_samples/uthsc_samples.py | 57 ++++++++++++++++++++++++++++++++
4 files changed, 95 insertions(+), 1 deletion(-)
create mode 100644 scripts/uthsc_samples/.gitignore
create mode 100644 scripts/uthsc_samples/template.yaml
create mode 100644 scripts/uthsc_samples/uthsc_samples.py
(limited to 'doc/blog')
diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org
index f3ba073..d0d6c7f 100644
--- a/doc/blog/using-covid-19-pubseq-part3.org
+++ b/doc/blog/using-covid-19-pubseq-part3.org
@@ -255,7 +255,8 @@ more metadata is yummy when stored in RDF. [[https://yummydata.org/][Yummydata]]
that many of the terms in above example are URIs, such as
host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606. We use
web ontologies for these to make the data less ambiguous and more
-FAIR. Check out the option fields as defined in the schema. If it is not listed
+FAIR. Check out the option fields as defined in the schema. If it is not listed,
+check the [[https://github.com/arvados/bh20-seq-resource/blob/master/semantic_enrichment/labels.ttl][labels.ttl]] file. Also,
a little bit of web searching may be required or [[./contact][contact]] us.
** Run the uploader (CLI)
diff --git a/scripts/uthsc_samples/.gitignore b/scripts/uthsc_samples/.gitignore
new file mode 100644
index 0000000..8786e3f
--- /dev/null
+++ b/scripts/uthsc_samples/.gitignore
@@ -0,0 +1 @@
+yaml
diff --git a/scripts/uthsc_samples/template.yaml b/scripts/uthsc_samples/template.yaml
new file mode 100644
index 0000000..1175ac8
--- /dev/null
+++ b/scripts/uthsc_samples/template.yaml
@@ -0,0 +1,35 @@
+id: placeholder
+
+license:
+ license_type: http://creativecommons.org/licenses/by/4.0/
+ title: "$sample_name - $locationx"
+ attribution_name: "Mariah Taylor, Colleen Jonsson"
+ attribution_url: https://www.uthsc.edu/medicine/molecular-sciences/faculty-directory/jonsson.php
+
+host:
+ host_id: "$sample_id"
+ host_species: http://purl.obolibrary.org/obo/NCBITaxon_9606
+
+sample:
+ sample_id: "$sample_id"
+ specimen_source: [http://purl.obolibrary.org/obo/NCIT_C155831]
+ collection_date: "$collection_date"
+ collection_location: $location
+
+virus:
+ virus_species: http://purl.obolibrary.org/obo/NCBITaxon_2697049
+ virus_strain: "$strain"
+
+technology:
+ sample_sequencing_technology: [http://www.ebi.ac.uk/efo/EFO_0008632]
+ sequence_assembly_method: https://bio.tools/BWA#!
+ additional_technology_information: Oxford Nanopore MiniIon RNA long reads
+
+submitter:
+ authors: [Mariah Taylor, Colleen Jonsson]
+ submitter_name: [Mariah Taylor, Colleen B. Jonsson, Pjotr Prins]
+ submitter_address: UTHSC, Memphis, Tennessee 38163, USA
+ originating_lab: Regional Biocontainment Laboratory, Memphis, TN
+ provider_sample_id: $sample_id
+ submitter_sample_id: $sample_id
+ submitter_orcid: [https://orcid.org/0000-0002-2640-7672,https://orcid.org/0000-0002-8021-9162]
diff --git a/scripts/uthsc_samples/uthsc_samples.py b/scripts/uthsc_samples/uthsc_samples.py
new file mode 100644
index 0000000..5c39398
--- /dev/null
+++ b/scripts/uthsc_samples/uthsc_samples.py
@@ -0,0 +1,57 @@
+import os
+import pandas as pd
+from string import Template
+from dateutil.parser import parse
+import re
+
+import sys
+
+# Metadata in tabular format in a spreadsheet(?!)
+xlsx = '../../test/data/10_samples.xlsx'
+
+# Template in a text file
+template_yaml = 'template.yaml'
+
+dir_output = 'yaml'
+
+if not os.path.exists(dir_output):
+ os.makedirs(dir_output)
+
+table = pd.read_excel(xlsx)
+
+print(table)
+
+for index, row in table.iterrows():
+ sample = row['Sample ID']
+ print(f"Processing sample {sample}...")
+
+ with open(template_yaml) as f:
+ text = Template(f.read())
+ with open(os.path.join(dir_output,f"{sample}.yaml"), 'w') as fw:
+ sample_id = sample
+ sample_name = sample
+ collection_date = parse(str(row['Collection Date'])).strftime('%Y-%m-%d')
+ locationx = row['City']+", "+row['State']+", USA"
+ location = "https://www.wikidata.org/wiki/Q16563" # Memphis by default
+ map = {
+ "Pegram": "https://www.wikidata.org/wiki/Q3289517",
+ "Alexander": "https://www.wikidata.org/wiki/Q79663",
+ "Smithville": "https://www.wikidata.org/wiki/Q2145339",
+ "Nashville": "https://www.wikidata.org/wiki/Q23197",
+ "Madison": "https://www.wikidata.org/wiki/Q494755"
+ }
+
+ for name in map:
+ p = re.compile(name)
+ if p.match(locationx):
+ location = map[name]
+ break
+
+ strain = f"SARS-CoV-2/human/USA/{sample}/2020"
+ fw.write(text.substitute(sample_id=sample_id,
+ sample_name=sample_name,
+ collection_date=collection_date,
+ location=location,
+ locationx=locationx,
+ strain=strain
+ ))
--
cgit v1.2.3
From 6eef898f8080e64a2eab9b60f54cacbd419c279e Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Tue, 10 Nov 2020 11:08:26 +0000
Subject: Document Arvados runner
---
doc/blog/using-covid-19-pubseq-part2.html | 127 +++++++++++++++---------------
doc/blog/using-covid-19-pubseq-part2.org | 21 +++++
2 files changed, 84 insertions(+), 64 deletions(-)
(limited to 'doc/blog')
diff --git a/doc/blog/using-covid-19-pubseq-part2.html b/doc/blog/using-covid-19-pubseq-part2.html
index 567980d..eff6fcd 100644
--- a/doc/blog/using-covid-19-pubseq-part2.html
+++ b/doc/blog/using-covid-19-pubseq-part2.html
@@ -3,7 +3,7 @@
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-
+
COVID-19 PubSeq - Arvados
@@ -40,7 +40,7 @@
}
pre.src {
position: relative;
- overflow: visible;
+ overflow: auto;
padding-top: 1.2em;
}
pre.src:before {
@@ -195,50 +195,26 @@
@@ -252,18 +228,18 @@ for the JavaScript code in this tag.
We are using Arvados to run common workflow language (CWL) pipelines.
@@ -283,8 +259,8 @@ workflows and the output of analysis pipelines (here CWL workflows).
-
-
2 The Arvados file interface
+
+
2 The Arvados file interface
Arvados has the web server, but it also has a REST API and associated
@@ -361,8 +337,8 @@ arv-get 2be6af7b4741f2a5c5f8ff2bc6152d73+1955623+Ab9ad65d7fe958a053b3a57d545839d
-
-
3 The PubSeq Arvados shell
+
+
3 The PubSeq Arvados shell
When you login to Arvados (you can request permission from us) it is
@@ -414,11 +390,34 @@ the git repo and starts a new run calling into
/data/pubseq/bh20-seq-resource/venv3/bin/bh20-seq-analyzer which is
essentially monitoring for uploads.
-Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp! Modified 2020-08-26 Wed 05:01.
+Created by Pjotr Prins (pjotr.public768 at thebird 'dot' nl) using Emacs org-mode and a healthy dose of Lisp! Modified 2020-11-09 Mon 01:20.
diff --git a/doc/blog/using-covid-19-pubseq-part2.org b/doc/blog/using-covid-19-pubseq-part2.org
index 4b827f5..d7816ba 100644
--- a/doc/blog/using-covid-19-pubseq-part2.org
+++ b/doc/blog/using-covid-19-pubseq-part2.org
@@ -96,6 +96,27 @@ the git repo and starts a new run calling into
/data/pubseq/bh20-seq-resource/venv3/bin/bh20-seq-analyzer which is
essentially [[https://github.com/arvados/bh20-seq-resource/blob/2baa88b766ec540bd34b96599014dd16e393af39/bh20seqanalyzer/main.py#L354][monitoring]] for uploads.
+On ~run --help~
+
+#+begin_example
+optional arguments:
+ -h, --help show this help message and exit
+ --uploader-project UPLOADER_PROJECT
+ --pangenome-analysis-project PANGENOME_ANALYSIS_PROJECT
+ --fastq-project FASTQ_PROJECT
+ --validated-project VALIDATED_PROJECT
+ --workflow-def-project WORKFLOW_DEF_PROJECT
+ --pangenome-workflow-uuid PANGENOME_WORKFLOW_UUID
+ --fastq-workflow-uuid FASTQ_WORKFLOW_UUID
+ --exclude-list EXCLUDE_LIST
+ --latest-result-collection LATEST_RESULT_COLLECTION
+ --kickoff
+ --no-start-analysis
+ --once
+ --print-status PRINT_STATUS
+ --revalidate
+#+end_example
+
* Wiring up CWL
In above script ~bh20-seq-analyzer~ you can see that the [[https://www.commonwl.org/][Common
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