From 73824fe1f94cb965f6de9d5b43bf2eb48241d3ea Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Tue, 27 Oct 2020 12:17:23 +0000
Subject: Updating docs

---
 doc/blog/using-covid-19-pubseq-part3.org | 22 ++++++++++++++++++++--
 1 file changed, 20 insertions(+), 2 deletions(-)

(limited to 'doc/blog/using-covid-19-pubseq-part3.org')

diff --git a/doc/blog/using-covid-19-pubseq-part3.org b/doc/blog/using-covid-19-pubseq-part3.org
index abc260c..fb68251 100644
--- a/doc/blog/using-covid-19-pubseq-part3.org
+++ b/doc/blog/using-covid-19-pubseq-part3.org
@@ -228,7 +228,25 @@ command line
 : python3 bh20sequploader/main.py example/sequence.fasta example/maximum_metadata_example.yaml
 
 after installing dependencies (also described in [[https://github.com/arvados/bh20-seq-resource/blob/master/doc/INSTALL.md][INSTALL]] with the GNU
-Guix package manager).
+Guix package manager). The ~--help~ shows
+
+#+begin_src sh
+Entering sequence uploader
+usage: main.py [-h] [--validate] [--skip-qc] [--trusted] metadata sequence_p1 [sequence_p2]
+
+Upload SARS-CoV-19 sequences for analysis
+
+positional arguments:
+  metadata     sequence metadata json
+  sequence_p1  sequence FASTA/FASTQ
+  sequence_p2  sequence FASTQ pair
+
+optional arguments:
+  -h, --help   show this help message and exit
+  --validate   Dry run, validate only
+  --skip-qc    Skip local qc check
+  --trusted    Trust local validation and add directly to validated project
+#+end_src
 
 The web interface using this exact same script so it should just work
 (TM).
@@ -265,4 +283,4 @@ and execute
 python3 esr_samples.py
 #+END_SRC
 
-You will find the YAML files in the `yaml` folder which will be created in the same directory.
\ No newline at end of file
+You will find the YAML files in the `yaml` folder which will be created in the same directory.
-- 
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