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Masifor230111 #301

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aef7574
started DR28 release notes
wwysoc2 Jan 29, 2021
6a24f44
Added scRNA documentation
wwysoc2 Feb 1, 2021
c5251be
Added release manifests
wwysoc2 Feb 2, 2021
b82780b
Corrected release notes
wwysoc2 Feb 2, 2021
0f21379
Merge pull request #104 from NCI-GDC/DR28
wwysoc2 Feb 2, 2021
3099231
Corrected release notes again
wwysoc2 Feb 2, 2021
b99eac6
Merge pull request #105 from NCI-GDC/DR28
wwysoc2 Feb 2, 2021
28ebbfd
indentation error
wwysoc2 Feb 2, 2021
75a3d3f
indentation error2
wwysoc2 Feb 2, 2021
724ce53
Added release notes + manifest for CPTAC-3
wwysoc2 Feb 4, 2021
661cfbb
Added release notes
wwysoc2 Feb 4, 2021
a6000fa
Merge pull request #107 from NCI-GDC/cptacmanifest
wwysoc2 Feb 4, 2021
9088248
Adding write-to-file
mforootan Feb 5, 2021
9ca8f1b
Create Adding_write_to_file.md
mforootan Feb 5, 2021
547562e
Update Adding_write_to_file.md
mforootan Feb 5, 2021
fd011f2
Update Adding_write_to_file.md
mforootan Feb 5, 2021
1484d43
Create Adding_write_to_file.md
mforootan Feb 5, 2021
3c9d5e1
Write-to-file Added
mforootan Feb 5, 2021
ec92e2c
Append Add to file
mforootan Feb 5, 2021
d60cc53
minor changes to Getting Started
mforootan Feb 8, 2021
632f40a
Added MAF manifest for CPTAC-3
wwysoc2 Feb 11, 2021
c2afc4d
Added release note about manifest
wwysoc2 Feb 11, 2021
5c728aa
Merge pull request #110 from NCI-GDC/MAFmanifestDR28-2
wwysoc2 Feb 11, 2021
9c2b9cf
update
purplepeopleeater Feb 16, 2021
cef7787
fix broken links
Mar 12, 2021
3e2f24d
Merge pull request #113 from NCI-GDC/March2021_links_updates
wwysoc2 Mar 12, 2021
fa62a53
tables should be separated
mforootan Mar 12, 2021
7307e76
Update Search_and_Retrieval.md
purplepeopleeater Mar 18, 2021
4bd1fd9
Update Search_and_Retrieval.md
purplepeopleeater Mar 18, 2021
ab96566
DAT-3003 redirect from dead authentication page link
singergr-ctds Feb 19, 2021
c1babda
Merge pull request #112 from NCI-GDC/DAT-3003/fix-404-redirect-page
singergr-ctds Mar 18, 2021
0b84a9a
snRNA clarification
wwysoc2 Mar 22, 2021
4f49577
DR 29 release notes
wwysoc2 Mar 22, 2021
bc02b5d
BEDPE and ASCAT tables corrected
mforootan Mar 26, 2021
615a644
Merge pull request #114 from NCI-GDC/masifor210312
wwysoc2 Mar 30, 2021
9e505de
Fixed numbering
wwysoc2 Mar 30, 2021
c957239
Merge pull request #115 from NCI-GDC/DR29
wwysoc2 Mar 30, 2021
4731522
Replaced curly quotations
wwysoc2 Mar 30, 2021
d42cf02
Replaced curly quotations again
wwysoc2 Mar 30, 2021
24f6c4d
formatting changes to WGS docs
wwysoc2 Mar 30, 2021
44bef15
formatting changes to WGS docs
wwysoc2 Mar 30, 2021
30894af
added manifests
wwysoc2 Mar 31, 2021
06c6e39
fixed manifest links
wwysoc2 Mar 31, 2021
f46ed8f
Fixed an italics issue
wwysoc2 Mar 31, 2021
ae6ffcc
Added file format title
wwysoc2 Mar 31, 2021
6c2f4b8
Fixed some formatting in DNA-Seq page
wwysoc2 Mar 31, 2021
9bd499c
Added parentheses
wwysoc2 Mar 31, 2021
94bb6a4
example update
purplepeopleeater Apr 5, 2021
69ff85b
doc updates
purplepeopleeater Apr 5, 2021
075049c
DTT_troubleshooting_update
purplepeopleeater Apr 9, 2021
d877e7b
supportable client info update
purplepeopleeater Apr 9, 2021
6d848f6
Update
purplepeopleeater Apr 9, 2021
5c2d2ff
Merge branch 'develop' into SV-1889_doc_update
wwysoc2 Apr 14, 2021
13f1c5c
Delete 1
wwysoc2 Apr 14, 2021
978a511
Merge pull request #117 from NCI-GDC/SV-1889_doc_update
wwysoc2 Apr 14, 2021
2bf0a35
update
purplepeopleeater Apr 26, 2021
5c12f76
Started Avery release notes
wwysoc2 May 11, 2021
124311f
image_update
purplepeopleeater May 14, 2021
c6b0a1a
exploration_updates
purplepeopleeater May 14, 2021
a34472f
image_update
purplepeopleeater May 14, 2021
08a3e25
Merge branch 'develop' into SV-1889_doc_update
wwysoc2 May 14, 2021
fe49a9a
Merge pull request #118 from NCI-GDC/SV-1889_doc_update
wwysoc2 May 14, 2021
102e448
Release Notes for Avery
wwysoc2 May 17, 2021
34bb612
Merge branch 'develop' into avery
wwysoc2 May 17, 2021
78dcda1
Merge pull request #119 from NCI-GDC/avery
wwysoc2 May 17, 2021
63463bc
update secrets
May 17, 2021
90dace4
updated miRNA seq and Submission QC sections with adapter trimming st…
May 18, 2021
a289aae
Boveri release notes
wwysoc2 Jun 17, 2021
bb5d971
Merge pull request #122 from NCI-GDC/boveri_dict
wwysoc2 Jun 17, 2021
1933d65
Changed Release Date
wwysoc2 Jun 18, 2021
702b47b
Added note about SV-1940
wwysoc2 Jun 22, 2021
c3727ef
Merge branch 'develop' into adapter-trim
wwysoc2 Jun 22, 2021
aad8a97
Merge pull request #121 from NCI-GDC/adapter-trim
wwysoc2 Jun 22, 2021
ef82830
Added release note about SV-1939
wwysoc2 Jul 8, 2021
e1d2ea1
Added ticket ref
wwysoc2 Jul 8, 2021
9653b2e
Merge pull request #124 from NCI-GDC/Dict-Release-Notes-Add
wwysoc2 Jul 8, 2021
f4b644d
Added Zhenyu's footnote on copy number values
Jul 8, 2021
402ce72
Merge pull request #125 from NCI-GDC/cnv_footnote
wwysoc2 Jul 21, 2021
85b5dd4
RPPA added
mforootan Jul 23, 2021
343c0ba
adding methylation array harmonization workflow to docs
Aug 6, 2021
0e5ca5f
fixed typo on methylation docs page
Aug 6, 2021
a57a400
RPPA added
mforootan Aug 17, 2021
1fb8a51
Merge branch 'develop' into masifor210817
wwysoc2 Aug 17, 2021
9c8dda6
Added dictionary release notes for Curie
wwysoc2 Aug 19, 2021
1dbd497
Added data portal release notes for Curie
wwysoc2 Aug 19, 2021
60e9b3b
Merge pull request #128 from NCI-GDC/CurieRelease
wwysoc2 Aug 19, 2021
3fb13fb
Changed RN date and added RN for DTT-UI
wwysoc2 Aug 23, 2021
fd4c24f
switched harmonization and LO sections around
Aug 30, 2021
8557f88
Merge pull request #126 from NCI-GDC/sesame_update
wwysoc2 Sep 10, 2021
c290d8a
Merge pull request #127 from NCI-GDC/masifor210817
wwysoc2 Sep 10, 2021
7505262
Added April/June 2021 notebooks to repo
wwysoc2 Sep 13, 2021
6159a57
Merge pull request #130 from NCI-GDC/first-jnotebooks
wwysoc2 Sep 13, 2021
23f0e52
Changed dir structure
wwysoc2 Sep 14, 2021
938544f
Updated Gencode Link
wwysoc2 Sep 16, 2021
d4e5602
DR 30 release notes
wwysoc2 Sep 23, 2021
89a5abd
Merge pull request #131 from NCI-GDC/DR30-RNs
wwysoc2 Sep 23, 2021
62e469f
Removed curly quotes
wwysoc2 Sep 23, 2021
684d024
Added RPPA page to build script
wwysoc2 Sep 24, 2021
5ab5507
Added two data release manifests
wwysoc2 Sep 24, 2021
f506594
added manifest files
wwysoc2 Sep 24, 2021
19083de
Merge pull request #132 from NCI-GDC/rppadocs
wwysoc2 Sep 24, 2021
b7cd072
added rna-seq note
wwysoc2 Sep 24, 2021
57e1795
Added example files to April Webinar
wwysoc2 Oct 12, 2021
85b3284
Added June webinar files
wwysoc2 Oct 12, 2021
edd41a2
Merge pull request #135 from NCI-GDC/notebook-files
wwysoc2 Oct 19, 2021
7b61d83
Initial DR31 release notes
wwysoc2 Oct 19, 2021
b5b5d2f
added release note date
wwysoc2 Oct 27, 2021
7152e42
Added list of slides with missing tiling
wwysoc2 Oct 28, 2021
5ea85f0
Added link to list of slides with missing tiling
wwysoc2 Oct 28, 2021
9893fda
Added caveat about slide image UUIDs
wwysoc2 Oct 28, 2021
276dd6a
Added manifest files to DR31 release notes
wwysoc2 Oct 29, 2021
d027777
Merge pull request #136 from NCI-GDC/dr31
wwysoc2 Oct 29, 2021
b6f68f3
Fixed JSON
wwysoc2 Oct 29, 2021
08672e1
Updates to RNA-Seq workflow
tzuni Feb 4, 2022
cbe1916
added some missing details
tzuni Feb 4, 2022
1c9c273
forgot to add images
tzuni Feb 4, 2022
f024d5d
Add ASCAT2, ascatNGS and GENIE CNV description
ZhenyuZ Feb 10, 2022
749caa8
removed Transcript Expression Counts from flowchart
tzuni Feb 28, 2022
8094648
Started release notes for DR32
wwysoc2 Feb 28, 2022
ff74b79
Merge pull request #140 from NCI-GDC/feat/gencode36_rnaseq
wwysoc2 Feb 28, 2022
0fb95d8
Small changes to RNA-docs
wwysoc2 Feb 28, 2022
eb301f3
Small changes to calc picture
wwysoc2 Feb 28, 2022
eeb6f0c
Margin on photo
wwysoc2 Feb 28, 2022
63e0cd9
Margin on photo
wwysoc2 Feb 28, 2022
cb1a2fa
Elongated photo
wwysoc2 Feb 28, 2022
2ae8379
Merge pull request #139 from ZhenyuZ/develop
wwysoc2 Feb 28, 2022
1756f5f
Release notes
wwysoc2 Feb 28, 2022
ec3b8bf
Merge pull request #141 from NCI-GDC/DR32_Release
wwysoc2 Feb 28, 2022
495592c
Rearranged CNV pipelines in document
wwysoc2 Mar 1, 2022
93069ef
Added MLO pipeline deprecation message.
wwysoc2 Mar 1, 2022
3967ab4
Added more release notes
wwysoc2 Mar 1, 2022
cfefa35
Added CNV release notes
wwysoc2 Mar 1, 2022
d632391
Added FM release notes
wwysoc2 Mar 1, 2022
d76d68b
Incorporate changes from SV-2094
wwysoc2 Mar 2, 2022
1e3eba3
Added changes from SV-2093
wwysoc2 Mar 2, 2022
0306ade
Removed character that was causing encoding errors.
wwysoc2 Mar 3, 2022
5728aa0
Added fancier RNA-Seq diagram
wwysoc2 Mar 3, 2022
b658e9b
Changes based on SV-2098
wwysoc2 Mar 7, 2022
d7127ca
More changes based on SV-2098
wwysoc2 Mar 7, 2022
fa82577
Added miRNA sentence
wwysoc2 Mar 8, 2022
b0546a2
Changed CL parameter to refer to v36
wwysoc2 Mar 8, 2022
3222849
Added missing aliquot TSV
wwysoc2 Mar 10, 2022
3118c74
Updated aliquot file
wwysoc2 Mar 10, 2022
8c540b4
A few changes and link to aliquot file
wwysoc2 Mar 10, 2022
21d7084
Added list of contaminated alignments.
wwysoc2 Mar 10, 2022
66f6b94
Changed date
wwysoc2 Mar 10, 2022
7eff305
Added bullet points
wwysoc2 Mar 10, 2022
67103a6
Fixed bullet points
wwysoc2 Mar 10, 2022
8dde7b6
Removed minor versions
wwysoc2 Mar 10, 2022
f5e05e7
Removed minor versions from RNA
wwysoc2 Mar 10, 2022
559dd66
Added methylation missing aliquot
wwysoc2 Mar 10, 2022
149cfea
Changes based on feedback from SV-2095
wwysoc2 Mar 10, 2022
4b4da00
Added more CNV info.
wwysoc2 Mar 15, 2022
ce60eff
Changed release date.
wwysoc2 Mar 15, 2022
ba9ee89
Added DR32 manifests
wwysoc2 Mar 16, 2022
06baf5d
Added links to DR32 manifests
wwysoc2 Mar 16, 2022
702c219
Feedback from FEAT-727
wwysoc2 Mar 17, 2022
bc850e9
Additions Explr page
wwysoc2 Mar 29, 2022
e5e58ba
Moved CNV point
wwysoc2 Mar 29, 2022
c56f810
Gencode v22-36 manifests
wwysoc2 Mar 29, 2022
87536de
Link to v22-36 manifests
wwysoc2 Mar 29, 2022
6df7586
changed header
wwysoc2 Mar 29, 2022
aa719de
Added failed DR33 aliquot
wwysoc2 May 2, 2022
0d21567
Release notes for DR33
wwysoc2 May 2, 2022
2a05d9b
Added DR33 manifests
wwysoc2 May 3, 2022
aeaf743
Changed links for new failed-aliquot file name
wwysoc2 May 3, 2022
94ea1c1
Merge pull request #143 from NCI-GDC/dr33
bullenc May 3, 2022
c62eaa0
Removed erroneous line
wwysoc2 May 3, 2022
2cf15bb
added exploration line
wwysoc2 May 3, 2022
4967ea5
Changed ensembl link
wwysoc2 May 3, 2022
bd8d852
Added MSIsensor notes
wwysoc2 May 9, 2022
6eafe7c
Changed Methylation Page name
wwysoc2 May 25, 2022
9a9524d
Added DR33.1 release notes
wwysoc2 May 25, 2022
8da0f08
Changed links per SV-1967
wwysoc2 May 31, 2022
cecec1a
Changed date on release notes.
wwysoc2 May 31, 2022
8415e67
Merge pull request #146 from NCI-GDC/msi
wwysoc2 May 31, 2022
d854c2f
Merge pull request #147 from NCI-GDC/DR331
wwysoc2 May 31, 2022
2e5d06e
Added defect line
wwysoc2 May 31, 2022
9927ccd
Merge pull request #148 from NCI-GDC/DR331
wwysoc2 May 31, 2022
b504950
Added DR33.1 manifest
wwysoc2 May 31, 2022
8bb0597
Merge pull request #149 from NCI-GDC/DR331
wwysoc2 May 31, 2022
7d2f5ed
Add HHS Vulnerability Disclosure link to footer
Jun 15, 2022
9cce60a
Merge pull request #151 from NCI-GDC/PEAR-379
wwysoc2 Jun 15, 2022
9d34c80
New array docs - clarifies TSV vs. JSON
wwysoc2 Jun 29, 2022
7c6f833
Image submission section added
mforootan Jul 1, 2022
58c4302
Merge branch 'develop' into masifor220630
wwysoc2 Jul 1, 2022
d4dbae4
Merge pull request #153 from NCI-GDC/masifor220630
wwysoc2 Jul 1, 2022
6804daf
Added clarification about TSV header
wwysoc2 Jul 1, 2022
ec5929b
Merge pull request #152 from NCI-GDC/NewArrayDocs
wwysoc2 Jul 1, 2022
09b3b01
Release notes
wwysoc2 Jul 1, 2022
6d435cb
Submission - Release notes
wwysoc2 Jul 1, 2022
6e37d59
API - Release notes
wwysoc2 Jul 1, 2022
0e93ed6
changed link number
wwysoc2 Jul 1, 2022
0529c9b
changed release year
wwysoc2 Jul 1, 2022
0702f02
Merge pull request #154 from NCI-GDC/DarwinRN
wwysoc2 Jul 1, 2022
83e2a4b
Added Release Notes
wwysoc2 Jul 8, 2022
dd45b59
Merge pull request #155 from NCI-GDC/DarwinRelease
wwysoc2 Jul 8, 2022
947fdcf
Release notes, DR34
wwysoc2 Jul 19, 2022
7cb2ebc
Fixing broken links in API section
wwysoc2 Jul 21, 2022
f3916e7
Fixed multiple links
wwysoc2 Jul 21, 2022
782517c
Merge pull request #157 from NCI-GDC/BrokenLinks_July2022
wwysoc2 Jul 22, 2022
6fd89d3
Update data release notes regarding DAT-3220
Jul 26, 2022
6cf0948
Update data release notes regarding DAT-3220
Jul 26, 2022
3b248e0
Merge pull request #158 from NCI-GDC/hcmi_aliquot_index_update
bullenc Jul 26, 2022
199ca8d
add dr34 manifest
Jul 27, 2022
0211027
Merge pull request #159 from NCI-GDC/add_dr34_mani
bullenc Jul 27, 2022
d11ca71
fix date
Jul 27, 2022
d2a2740
Merge pull request #161 from NCI-GDC/fix_date
bullenc Jul 27, 2022
21b6f35
broken links updated
Sep 7, 2022
ca56e57
Merge pull request #163 from NCI-GDC/update_broken_links
bullenc Sep 7, 2022
acd9f1b
Start of release notes
wwysoc2 Sep 7, 2022
93b3fac
Removed SomaticSniper Content
wwysoc2 Sep 12, 2022
a317f1a
DR35-HTSeq files removed
mforootan Sep 13, 2022
f47a087
DR35 - FPKM files updated
mforootan Sep 13, 2022
5b7b050
Merge pull request #164 from NCI-GDC/masifor220913
wwysoc2 Sep 13, 2022
1f0d765
Removed SomaticSniper from encyclopedia
wwysoc2 Sep 14, 2022
d10bbb1
Fixed somaticsniper sentence.
wwysoc2 Sep 14, 2022
b756d10
Changed column def in MAF docs.
wwysoc2 Sep 14, 2022
93c3298
Clarified RNA-Seq data
wwysoc2 Sep 14, 2022
cad9240
Merge pull request #165 from NCI-GDC/DR35
wwysoc2 Sep 16, 2022
d1b4ba3
updated encyclo page
Sep 16, 2022
1915365
added release notes link for DR35
Sep 16, 2022
b38e001
added release notes link for DR35
Sep 16, 2022
c8216b6
Merge pull request #166 from NCI-GDC/DR35_2
bullenc Sep 16, 2022
cacdc47
release note update on TARGET demo clin data update
Sep 23, 2022
4e2986d
fix link
Sep 23, 2022
2c079d6
Merge pull request #167 from NCI-GDC/fix_link
bullenc Sep 23, 2022
4203ea7
fixed image and manifest links
Sep 26, 2022
5e91e50
Merge pull request #168 from NCI-GDC/fix_links
bullenc Sep 26, 2022
6b1d565
update dr35 release date and active portal manifest file
Sep 28, 2022
7175a2a
Merge pull request #169 from NCI-GDC/dr35_date_mani_update
bullenc Sep 28, 2022
737fcaa
fix version in mani link
Sep 28, 2022
5c6394c
Merge pull request #170 from NCI-GDC/fix_version
bullenc Sep 28, 2022
a8d7e56
updated the num processes flag options for command line DTT
Oct 14, 2022
9d228f0
updates to gencode version and example BAM uuids
Oct 17, 2022
8f8fc40
Merge pull request #172 from NCI-GDC/bam_slice_api_doc_gencode_update
bullenc Oct 17, 2022
63b87be
Merge pull request #173 from NCI-GDC/fix_DTT_n_processes
bullenc Oct 17, 2022
008ba78
Mutation Issue release notes
wwysoc2 Dec 5, 2022
67b0ed9
Merge pull request #175 from NCI-GDC/mutation_rns
wwysoc2 Dec 5, 2022
3c0ad04
DR36 release notes
wwysoc2 Dec 12, 2022
dc39cba
CNV info
wwysoc2 Dec 12, 2022
76fe3c1
changed manifest name
wwysoc2 Dec 12, 2022
f41367d
Removed mutation index bug
wwysoc2 Dec 12, 2022
51368fd
Merge pull request #178 from NCI-GDC/DR36-RNs
wwysoc2 Dec 12, 2022
8943934
added DR36 release manifest
Dec 12, 2022
15a9563
moved dr36 mani to correct dir
Dec 12, 2022
0bcff9d
moved dr36 mani to correct dir
Dec 12, 2022
ac84c80
corrections to release notes
wwysoc2 Dec 12, 2022
192df72
Added bisulfite seq manifests
wwysoc2 Dec 12, 2022
12b9ad7
A word document also sent to BW
mforootan Jan 17, 2023
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6 changes: 6 additions & 0 deletions .pre-commit-config.yaml
Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
repos:
- repo: [email protected]:Yelp/detect-secrets
rev: v0.13.1
hooks:
- id: detect-secrets
args: ['--baseline', '.secrets.baseline']
248 changes: 248 additions & 0 deletions .secrets.baseline
Original file line number Diff line number Diff line change
@@ -0,0 +1,248 @@
{
"exclude": {
"files": null,
"lines": null
},
"generated_at": "2022-07-21T19:58:35Z",
"plugins_used": [
{
"name": "AWSKeyDetector"
},
{
"name": "ArtifactoryDetector"
},
{
"base64_limit": 4.5,
"name": "Base64HighEntropyString"
},
{
"name": "BasicAuthDetector"
},
{
"name": "CloudantDetector"
},
{
"hex_limit": 3,
"name": "HexHighEntropyString"
},
{
"name": "IbmCloudIamDetector"
},
{
"name": "IbmCosHmacDetector"
},
{
"name": "JwtTokenDetector"
},
{
"keyword_exclude": null,
"name": "KeywordDetector"
},
{
"name": "MailchimpDetector"
},
{
"name": "PrivateKeyDetector"
},
{
"name": "SlackDetector"
},
{
"name": "SoftlayerDetector"
},
{
"name": "StripeDetector"
},
{
"name": "TwilioKeyDetector"
}
],
"results": {
"docs/API/Users_Guide/Additional_Examples.md": [
{
"hashed_secret": "d9bbc424159a2c5ef89902e02caa2be6cff1817c",
"is_secret": false,
"is_verified": false,
"line_number": 89,
"type": "Hex High Entropy String"
},
{
"hashed_secret": "34d2afab6dc6f76855d5f83cc2dbed2efd99ddfb",
"is_secret": false,
"is_verified": false,
"line_number": 110,
"type": "Hex High Entropy String"
}
],
"docs/API/Users_Guide/Getting_Started.md": [
{
"hashed_secret": "05b339a29ce9a548e1efbe032131cfcdde6727d8",
"is_secret": false,
"is_verified": false,
"line_number": 91,
"type": "Hex High Entropy String"
}
],
"docs/API/Users_Guide/Search_and_Retrieval.md": [
{
"hashed_secret": "e9813ab1054cec827e517760617ac33bd97af1f3",
"is_secret": false,
"is_verified": false,
"line_number": 307,
"type": "Hex High Entropy String"
},
{
"hashed_secret": "22ecc0fefa20bdbbdff52cdd35fad2974db02e56",
"is_secret": false,
"is_verified": false,
"line_number": 353,
"type": "Hex High Entropy String"
},
{
"hashed_secret": "8b0471397a6dec83405ee2ae28edde87d02271a0",
"is_secret": false,
"is_verified": false,
"line_number": 389,
"type": "Hex High Entropy String"
},
{
"hashed_secret": "14f469780554b9dd75a3d03a267b3be725582499",
"is_secret": false,
"is_verified": false,
"line_number": 422,
"type": "Hex High Entropy String"
},
{
"hashed_secret": "6b505580b5bc4fab5bd4b2e0e10d621fea0614ee",
"is_secret": false,
"is_verified": false,
"line_number": 465,
"type": "Hex High Entropy String"
},
{
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1 change: 1 addition & 0 deletions API_UG.yml
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Expand Up @@ -16,6 +16,7 @@ pages:
- BAM Slicing: 'API/Users_Guide/BAM_Slicing.md'
- Submission: 'API/Users_Guide/Submission.md'
- Python Examples: 'API/Users_Guide/Python_Examples.md'
- GraphQL Examples: 'API/Users_Guide/GraphQL_Examples.md'
- System Information: 'API/Users_Guide/System_Information.md'
- Additional Examples: 'API/Users_Guide/Additional_Examples.md'
- "Appendix A: Available Fields": 'API/Users_Guide/Appendix_A_Available_Fields.md'
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14 changes: 14 additions & 0 deletions Adding_write_to_file.md
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@@ -0,0 +1,14 @@
# Changes made 2-5-2021

An extra script added to the following scripts, to redirect a copy of the output to a file:

```
- A Basic Query

- A Filtered Query

- Complex Filters

- Basic Troubleshooting
```
Also the ```.PY``` files in ```scripts``` folder were updated accordingly.
18 changes: 6 additions & 12 deletions Data_Submission_Portal_UG.yml
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Expand Up @@ -9,19 +9,13 @@ copyright: "© 2015-2016"
theme_dir: theme
pages:
- Data Submission Portal:
- Getting Started: 'Data_Submission_Portal/Users_Guide/Getting_Started.md'
- Submission Workflow: 'Data_Submission_Portal/Users_Guide/Submission_Workflow.md'
- Authentication: 'Data_Submission_Portal/Users_Guide/Authentication.md'
- Homepage: 'Data_Submission_Portal/Users_Guide/Homepage.md'
- Dashboard: 'Data_Submission_Portal/Users_Guide/Dashboard.md'
- Upload Data: 'Data_Submission_Portal/Users_Guide/Data_Upload_UG.md'
- Submit Data: 'Data_Submission_Portal/Users_Guide/Submit_Data.md'
- Release Data: 'Data_Submission_Portal/Users_Guide/Release_Data.md'
- Transactions: 'Data_Submission_Portal/Users_Guide/Transactions.md'
- Browse Data: 'Data_Submission_Portal/Users_Guide/Browse_Data.md'
- Pre-Release Data Review: 'Data_Submission_Portal/Users_Guide/Pre_Release_QC.md'
- Best Practices: 'Data_Submission_Portal/Users_Guide/Best_Practices.md'
- Before Submitting Data to the GDC Portal: 'Data_Submission_Portal/Users_Guide/Checklist.md'
- Data Submission Overview: 'Data_Submission_Portal/Users_Guide/Data_Submission_Overview.md'
- Data Submission Portal: 'Data_Submission_Portal/Users_Guide/Data_Submission_Process.md'
- Data Upload Walkthrough: 'Data_Submission_Portal/Users_Guide/Data_Submission_Walkthrough.md'
- Pre-Release Data Portal: 'Data_Submission_Portal/Users_Guide/Pre_Release_QC.md'
- Release Notes: 'Data_Submission_Portal/Release_Notes/Data_Submission_Portal_Release_Notes.md'

extra:
project_root_dir: '/'
project_org: 'GDC'
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6 changes: 2 additions & 4 deletions Data_Transfer_Tool_UG.yml
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Expand Up @@ -10,12 +10,10 @@ theme_dir: theme
pages:
- Data Transfer Tool:
- Getting Started: 'Data_Transfer_Tool/Users_Guide/Getting_Started.md'
- Accessing Built-in Help: 'Data_Transfer_Tool/Users_Guide/Accessing_Built-in_Help.md'
- Preparing for Data Download and Upload: 'Data_Transfer_Tool/Users_Guide/Preparing_for_Data_Download_and_Upload.md'
- Data Download and Upload - Command Line: 'Data_Transfer_Tool/Users_Guide/Data_Download_and_Upload.md'
- Data Download - UI: 'Data_Transfer_Tool/Users_Guide/Data_Download_Upload_UI.md'
- Key Terms: 'Data_Transfer_Tool/Users_Guide/Appendix_A_-_Key_Terms.md'
- Data Transfer Tool Command Line Documentation: 'Data_Transfer_Tool/Users_Guide/Data_Download_and_Upload.md'
- Release Notes - Command Line: 'Data_Transfer_Tool/Release_Notes/DTT_Release_Notes.md'
- Data Transfer Tool UI Documentation: 'Data_Transfer_Tool/Users_Guide/Data_Download_DTT_UI.md'
- Release Notes - UI: 'Data_Transfer_Tool/Release_Notes/DTT_UI_Release_Notes.md'

extra:
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4 changes: 3 additions & 1 deletion Data_UG.yml
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Expand Up @@ -18,7 +18,9 @@ pages:
- "Bioinformatics Pipeline: mRNA Analysis": 'Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline.md'
- "Bioinformatics Pipeline: miRNA Analysis": 'Data/Bioinformatics_Pipelines/miRNA_Pipeline.md'
- "Bioinformatics Pipeline: Copy Number Variation": 'Data/Bioinformatics_Pipelines/CNV_Pipeline.md'
- "Bioinformatics Pipeline: Methylation Liftover": 'Data/Bioinformatics_Pipelines/Methylation_LO_Pipeline.md'
- "Bioinformatics Pipeline: Methylation Analysis": 'Data/Bioinformatics_Pipelines/Methylation_Pipeline.md'
- "Bioinformatics Pipeline: Protein Expression": 'Data/Bioinformatics_Pipelines/RPPA_intro.md'
- Aligned Reads Summary Metrics: 'Data/Bioinformatics_Pipelines/Aligned_reads_summary_metrics.md'
- Release Notes: 'Data/Release_Notes/Data_Release_Notes.md'
extra:
project_root_dir: '/'
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