generated from CDCgov/template
-
Notifications
You must be signed in to change notification settings - Fork 10
/
gisaid_cov_submission.Rmd
194 lines (131 loc) · 7.08 KB
/
gisaid_cov_submission.Rmd
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
---
output: rmarkdown::html_document
title: "GISAID - EpiCoV"
vignette: >
%\VignetteIndexEntry{GISAID - EpiCoV}
%\VignetteEngine{knitr::rmarkdown}
%\VignetteEncoding{UTF-8}
---
<style>
table {
border: none;
}
td, th, tr {
border: 1px solid gray;
padding: 5px 5px 5px 5px;
}
</style>
```{r, include=FALSE, echo=FALSE, message=FALSE, warning=FALSE}
# R libraries
library(knitr) # for html table
library(yaml) # for yaml file
library(tidyverse) # for pipe
library(reshape2) # for data manipulation
# Read in the DESCRIPTION file
description <- yaml::read_yaml("../DESCRIPTION")
# Define variables
program <- description$Package
title <- "EpiCoV"
prefix <- "gs-"
cli <- "covCLI"
cli_list <- c("EpiFlu", "EpiCoV", "EpiRSV", "EpiArbo")
portals <- c("NCBI", "NCBI", "NCBI", "GISAID", "GISAID")
databases <- c("BIOSAMPLE", "SRA", "GENBANK", "FLU", "COV")
organism <- c("SARS-COV-2")
organism_abbrev <- c("COV")
# Define github repo
github_repo <- description$URL
# Define github pages URL
github_pages_url <- description$GITHUB_PAGES
# Create main config data frame
main_config_df <- data.frame(
portals = portals,
databases = databases
) %>%
dplyr::filter(
databases %in% toupper(!!organism_abbrev)
)
# Read in data files
main_config_file <- yaml::read_yaml("../config/main_config.yaml")
# Store all required fields
metadata_df <- reshape2::melt(main_config_file$SUBMISSION_PORTAL$COMMON_FIELDS) %>%
dplyr::transmute(
Column_name = gsub("[*&?#]", "", L1),
Description = value
)
# Combine all fields in given databases and portals
for(d in 1:nrow(main_config_df)){
#d=1
database <- main_config_df$databases[d]
portal <- main_config_df$portals[which(main_config_df$databases %in% database)]
if("COMMON_FIELDS" %in% names(main_config_file$SUBMISSION_PORTAL$PORTAL_NAMES[[portal]])){
portal_fields <- reshape2::melt(main_config_file$SUBMISSION_PORTAL$PORTAL_NAMES[[portal]]$COMMON_FIELDS) %>%
dplyr::transmute(
Column_name = gsub("[*&?#]", "", L1),
Description = value
)
metadata_df <- metadata_df %>%
dplyr::bind_rows(portal_fields) %>%
dplyr::distinct(.keep_all = TRUE)
}
database_fields <- reshape2::melt(main_config_file$SUBMISSION_PORTAL$PORTAL_NAMES[[portal]]$DATABASE[[database]]) %>%
dplyr::transmute(
Column_name = gsub("[*&?#]", "", L1),
Description = value
)
metadata_df <- metadata_df %>%
dplyr::bind_rows(database_fields) %>%
dplyr::distinct(.keep_all = TRUE)
}
optional_attributes_df <- read.csv("./data/cov_metadata_optional_fields.csv", header=TRUE)
```
## Overview
**GISAID**, short for the **Global Initiative on Sharing All Influenza Data**, is an organization that manages a restricted-access database containing genomic sequence data of select virus, primarily influenza viruses. The database has expanded to include the coronavirus responsible for the COVID-19 pandemic as well as other pathogens.
## Prerequisites
For all GISAID submissions, ``r program`` makes use of GISAID's Command Line Interface Tools (CLIs) to batch uploading meta- and sequence-data to their databases. Prior to perform a batch upload to **`r title` database**, submitters must
1. Download the **`r paste(title, "CLI")`** package from the **GISAID Platform** that is compatible with their machine (e.g., Linux, macOS, or Windows).
<br>
2. Unzip the downloaded package and store it in a subfolder called **`gisaid_cli`** within a submission directory of choice (e.g., `submission_dir`).
<br>
## Requirement files
After submitters had obtained the **GISAID CLI** for **`r title`**, they must also prepare the requirement files (such as `config.yaml`, `metadata.csv`, `sequence.fasta`, `raw reads`, etc.) and store them in a submission folder of choice (e.g., `submission_name`) within a parent submission directory (e.g., `submission_dir`). That way ``r program`` will be able to scoop up the necessary files in that folder, generate submission files, and then batch uploading them to the submitting database of choices.
Here is a list of the requirement files and where to store them:
- [Config file](#config-file) in a `yaml` format
- [Fasta file](#fasta-file) in a`fasta` format
- [Metadata file](#metadata-file) in a `csv` format
### Config file
Config file is a yaml file that provides a brief description about the submission and contains user credentials that allow ``r program`` to authenticate the database prior to upload a submission.
:::{style="padding: 10px; border: 1px solid blue !important;"}
<i class="fas fa-triangle-exclamation" role="presentation" aria-label="triangle-exclamation icon"></i> **NOTE:** <br>
- To submit to NCBI only, one can remove the **GISAID Submission (b)** section from the config file. Vice versa, to submit to GISAID only, just remove the **NCBI Submission (a)** section. <br>
- **Submission_Position** determines the order of databases in which we will submit to first. For instance, if GISAID is set as `1`, **_`r program`_** will submit to GISAID first, then after all samples are assigned with a GISAID accession number, **_`r program`_** will proceed to submit to NCBI. This order of submission ensures samples are linked correctly between the two databases. <br>
- **Username** and **Password** under the **NCBI Submission (b)** section are the credentials used to authenticate the **NCBI FTP Server** (not to mistake with individual NCBI account). See [PRE-REQUISITES](`r github_pages_url`/index.html#prerequisites) for more details.
:::
### Fasta file
Fasta file contains nucleotide sequences for all samples. See [Genbank Fasta Format](https://www.ncbi.nlm.nih.gov/genbank/fastaformat/) for more details.
### Metadata file
The metadata worksheet is a comma-delimited (csv) file that contains required attributes that are useful for the rapid analysis and trace back of **`r paste0(organism, collapse=" or ")`** cases.
Here is a short description about the fields in the metadata worksheet.
```{r include=TRUE, echo=FALSE, message=FALSE, warning=FALSE}
knitr::kable(metadata_df, format = "html", row.names = FALSE, escape = FALSE)
```
<br>
**NOTE:** The prefix of **“`r prefix`”** is used to identity attributes for **GISAID** submissions.
<br>
#### <b>Optional Attributes</b>
To include additional attributes to **`r title`** submissions, just append ``r prefix`` in front of the desired attributes. Here is a list of optional attributes:
```{r include=TRUE, echo=FALSE, message=FALSE, warning=FALSE}
knitr::kable(optional_attributes_df, format = "html", row.names = FALSE, escape = FALSE)
```
<br>
<br><br>
<p style="font-size: 20px">[*<i class="fas fa-play" role="presentation" aria-label="play icon"></i> You are now ready to install ``r program`` and batch upload your submission*](`r github_pages_url`/articles/local_installation.html)</p>
<br><br><br>
Any questions or issues? Please report them on our <a href="`r github_repo`/issues" target="_blank">Github issue tracker</a>.
<br>