Skip to content

Commit

Permalink
Merge pull request #23 from CDCgov/final-merged
Browse files Browse the repository at this point in the history
Final merged with added fixes to citations, license, program version, added optional tables, etc.
  • Loading branch information
rchau88 committed Feb 9, 2024
2 parents 9b8b46f + 44d04a7 commit a573a1d
Show file tree
Hide file tree
Showing 141 changed files with 15,157 additions and 8,183 deletions.
2 changes: 2 additions & 0 deletions .Rbuildignore
Original file line number Diff line number Diff line change
@@ -0,0 +1,2 @@
^.*\.Rproj$
^\.Rproj\.user$
1 change: 1 addition & 0 deletions .Rproj.user/39CB7C5D/cpp-definition-cache
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
[]
9 changes: 9 additions & 0 deletions .Rproj.user/39CB7C5D/pcs/files-pane.pper
Original file line number Diff line number Diff line change
@@ -0,0 +1,9 @@
{
"sortOrder": [
{
"columnIndex": 2,
"ascending": true
}
],
"path": "~/Github/seqsender/docs/articles"
}
4 changes: 4 additions & 0 deletions .Rproj.user/39CB7C5D/pcs/source-pane.pper
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
{
"activeTab": 1,
"activeTabSourceWindow0": 2
}
14 changes: 14 additions & 0 deletions .Rproj.user/39CB7C5D/pcs/windowlayoutstate.pper
Original file line number Diff line number Diff line change
@@ -0,0 +1,14 @@
{
"left": {
"splitterpos": 315,
"topwindowstate": "NORMAL",
"panelheight": 892,
"windowheight": 966
},
"right": {
"splitterpos": 580,
"topwindowstate": "NORMAL",
"panelheight": 892,
"windowheight": 966
}
}
5 changes: 5 additions & 0 deletions .Rproj.user/39CB7C5D/pcs/workbench-pane.pper
Original file line number Diff line number Diff line change
@@ -0,0 +1,5 @@
{
"TabSet1": 0,
"TabSet2": 0,
"TabZoom": {}
}
11 changes: 11 additions & 0 deletions .Rproj.user/39CB7C5D/persistent-state
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
activeClientUrl="http://localhost:8787/"
build-last-errors="[]"
build-last-errors-base-dir=""
build-last-outputs="[]"
compile_pdf_state="{\"tab_visible\":false,\"running\":false,\"target_file\":\"\",\"output\":\"\",\"errors\":[]}"
displayName="snu3"
files.monitored-path=""
find-in-files-state="{\"handle\":\"\",\"input\":\"\",\"path\":\"\",\"regex\":false,\"ignoreCase\":false,\"results\":{\"file\":[],\"line\":[],\"lineValue\":[],\"matchOn\":[],\"matchOff\":[],\"replaceMatchOn\":[],\"replaceMatchOff\":[]},\"running\":false,\"replace\":false,\"preview\":false,\"gitFlag\":false,\"replacePattern\":\"\"}"
imageDirtyState="1"
portToken="a60fe80fe2a7"
saveActionState="-1"
1 change: 1 addition & 0 deletions .Rproj.user/39CB7C5D/saved_source_markers
Original file line number Diff line number Diff line change
@@ -0,0 +1 @@
{"active_set":"","sets":[]}
6 changes: 6 additions & 0 deletions .Rproj.user/39CB7C5D/sources/prop/0476E19C
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
{
"source_window_id": "",
"Source": "Source",
"cursorPosition": "12,0",
"scrollLine": "0"
}
6 changes: 6 additions & 0 deletions .Rproj.user/39CB7C5D/sources/prop/11FFA47D
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
{
"source_window_id": "",
"Source": "Source",
"cursorPosition": "18,0",
"scrollLine": "0"
}
6 changes: 6 additions & 0 deletions .Rproj.user/39CB7C5D/sources/prop/133055F3
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
{
"source_window_id": "",
"Source": "Source",
"cursorPosition": "18,3",
"scrollLine": "2"
}
6 changes: 6 additions & 0 deletions .Rproj.user/39CB7C5D/sources/prop/145F7FB1
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
{
"source_window_id": "",
"Source": "Source",
"cursorPosition": "18,3",
"scrollLine": "0"
}
6 changes: 6 additions & 0 deletions .Rproj.user/39CB7C5D/sources/prop/23CF97DB
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
{
"source_window_id": "",
"Source": "Source",
"cursorPosition": "11,0",
"scrollLine": "4"
}
6 changes: 6 additions & 0 deletions .Rproj.user/39CB7C5D/sources/prop/31DDB8C3
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
{
"source_window_id": "",
"Source": "Source",
"cursorPosition": "18,3",
"scrollLine": "0"
}
6 changes: 6 additions & 0 deletions .Rproj.user/39CB7C5D/sources/prop/852CBDEC
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
{
"source_window_id": "",
"Source": "Source",
"cursorPosition": "133,7",
"scrollLine": "128"
}
6 changes: 6 additions & 0 deletions .Rproj.user/39CB7C5D/sources/prop/8D5998D2
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
{
"source_window_id": "",
"Source": "Source",
"cursorPosition": "41,0",
"scrollLine": "11"
}
6 changes: 6 additions & 0 deletions .Rproj.user/39CB7C5D/sources/prop/8D7E8C0C
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
{
"source_window_id": "",
"Source": "Source",
"cursorPosition": "18,3",
"scrollLine": "0"
}
6 changes: 6 additions & 0 deletions .Rproj.user/39CB7C5D/sources/prop/96F7E2CE
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
{
"source_window_id": "",
"Source": "Source",
"cursorPosition": "11,1",
"scrollLine": "0"
}
6 changes: 6 additions & 0 deletions .Rproj.user/39CB7C5D/sources/prop/A381AFDE
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
{
"source_window_id": "",
"Source": "Source",
"cursorPosition": "135,7",
"scrollLine": "118"
}
4 changes: 4 additions & 0 deletions .Rproj.user/39CB7C5D/sources/prop/CA2A269A
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
{
"source_window_id": "",
"Source": "Source"
}
6 changes: 6 additions & 0 deletions .Rproj.user/39CB7C5D/sources/prop/CB36CFA0
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
{
"source_window_id": "",
"Source": "Source",
"cursorPosition": "130,7",
"scrollLine": "117"
}
6 changes: 6 additions & 0 deletions .Rproj.user/39CB7C5D/sources/prop/ED898A07
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
{
"source_window_id": "",
"Source": "Source",
"cursorPosition": "159,7",
"scrollLine": "148"
}
6 changes: 6 additions & 0 deletions .Rproj.user/39CB7C5D/sources/prop/FB37969B
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
{
"source_window_id": "",
"Source": "Source",
"cursorPosition": "4,0",
"scrollLine": "0"
}
21 changes: 21 additions & 0 deletions .Rproj.user/39CB7C5D/sources/prop/INDEX
Original file line number Diff line number Diff line change
@@ -0,0 +1,21 @@
~%2FGithub%2Fseqsender%2F.gitignore="11FFA47D"
~%2FGithub%2Fseqsender%2FDESCRIPTION="8D5998D2"
~%2FGithub%2Fseqsender%2FLICENSE="CA2A269A"
~%2FGithub%2Fseqsender%2FNEWS.md="FB37969B"
~%2FGithub%2Fseqsender%2FREADME.Rmd="707D8EA7"
~%2FGithub%2Fseqsender%2F_pkgdown.yml="0476E19C"
~%2FGithub%2Fseqsender%2Fconfig%2Fmain_config.yaml="67478E68"
~%2FGithub%2Fseqsender%2Finst%2FCITATION="96F7E2CE"
~%2FGithub%2Fseqsender%2Fvignettes%2Fbiosample_submission.Rmd="133055F3"
~%2FGithub%2Fseqsender%2Fvignettes%2Fcompose_installation.Rmd="852CBDEC"
~%2FGithub%2Fseqsender%2Fvignettes%2Fdocker_installation.Rmd="CB36CFA0"
~%2FGithub%2Fseqsender%2Fvignettes%2Ffaqs.Rmd="DE820693"
~%2FGithub%2Fseqsender%2Fvignettes%2Fgenbank_submission.Rmd="8D7E8C0C"
~%2FGithub%2Fseqsender%2Fvignettes%2Fgisaid_cov_submission.Rmd="145F7FB1"
~%2FGithub%2Fseqsender%2Fvignettes%2Fgisaid_flu_submission.Rmd="23CF97DB"
~%2FGithub%2Fseqsender%2Fvignettes%2Fgisaid_options.Rmd="ABEE9B5E"
~%2FGithub%2Fseqsender%2Fvignettes%2Flocal_installation.Rmd="ED898A07"
~%2FGithub%2Fseqsender%2Fvignettes%2Fprerequisites.Rmd="3EA705BD"
~%2FGithub%2Fseqsender%2Fvignettes%2Fsingularity_installation.Rmd="A381AFDE"
~%2FGithub%2Fseqsender%2Fvignettes%2Fsra_options.Rmd="D3D73A1D"
~%2FGithub%2Fseqsender%2Fvignettes%2Fsra_submission.Rmd="31DDB8C3"
26 changes: 26 additions & 0 deletions .Rproj.user/39CB7C5D/sources/session-644ed55e/042D06D7
Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
{
"id": "042D06D7",
"path": "~/Github/seqsender/NEWS.md",
"project_path": "NEWS.md",
"type": "markdown",
"hash": "427892802",
"contents": "",
"dirty": false,
"created": 1707162056710.0,
"source_on_save": false,
"relative_order": 12,
"properties": {
"source_window_id": "",
"Source": "Source",
"cursorPosition": "4,0",
"scrollLine": "0"
},
"folds": "",
"lastKnownWriteTime": 1707499282,
"encoding": "UTF-8",
"collab_server": "",
"source_window": "",
"last_content_update": 1707499282031,
"read_only": false,
"read_only_alternatives": []
}
Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@

# seqsender 1.1.0
* Github Repo: https://github.com/CDCgov/seqsender
* Documentation: https://cdcgov.github.io/seqsender
26 changes: 26 additions & 0 deletions .Rproj.user/39CB7C5D/sources/session-644ed55e/0CBC917E
Original file line number Diff line number Diff line change
@@ -0,0 +1,26 @@
{
"id": "0CBC917E",
"path": "~/Github/seqsender/vignettes/compose_installation.Rmd",
"project_path": "vignettes/compose_installation.Rmd",
"type": "r_markdown",
"hash": "1875304587",
"contents": "",
"dirty": false,
"created": 1707157109242.0,
"source_on_save": false,
"relative_order": 9,
"properties": {
"source_window_id": "",
"Source": "Source",
"cursorPosition": "133,7",
"scrollLine": "128"
},
"folds": "",
"lastKnownWriteTime": 1707512280,
"encoding": "UTF-8",
"collab_server": "",
"source_window": "",
"last_content_update": 1707512280458,
"read_only": false,
"read_only_alternatives": []
}
Loading

0 comments on commit a573a1d

Please sign in to comment.