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Rc test slideseq kickoff #1477

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4f6caf4
grabbranch name
nikellepetrillo Dec 12, 2024
5201638
grabbranch name
nikellepetrillo Dec 12, 2024
8bc8620
grabbranch name
nikellepetrillo Dec 12, 2024
1851489
grabbranch name
nikellepetrillo Dec 12, 2024
4f3c8a2
grabbranch name
nikellepetrillo Dec 12, 2024
c25eba5
grabbranch name
nikellepetrillo Dec 12, 2024
585fe24
grabbranch name
nikellepetrillo Dec 12, 2024
ee3acee
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
14c30eb
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
b43467c
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
6583b6e
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
43dc17b
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
53409b1
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
719ab22
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
c28727c
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
36fa9ce
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
f7093c7
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
30d0f22
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
543c16a
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
e5ea29a
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
1742d24
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
439b0f9
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
bf5203e
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
3e2fe45
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
b2240ea
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
5c5614c
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
105c9a3
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
22334ec
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
a102049
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
118862d
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
147d560
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
856446e
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
1f82168
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
3da5800
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
9bcc126
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
d1d14c0
try to auth so we can gsutilc cp
nikellepetrillo Dec 13, 2024
c322ff6
try to auth so we can gsutilc cp
nikellepetrillo Dec 18, 2024
a49e1df
try creating a new method config for each branch
nikellepetrillo Dec 18, 2024
be92317
try creating a new method config for each branch
nikellepetrillo Dec 18, 2024
2c3799d
try creating a new method config for each branch
nikellepetrillo Dec 18, 2024
4879556
try creating a new method config for each branch
nikellepetrillo Dec 18, 2024
80dce50
try creating a new method config for each branch
nikellepetrillo Dec 18, 2024
87491a0
try creating a new method config for each branch
nikellepetrillo Dec 18, 2024
0e1bb1c
try creating a new method config for each branch
nikellepetrillo Dec 18, 2024
9eff909
put not post
nikellepetrillo Dec 18, 2024
33826f9
put not post
nikellepetrillo Dec 18, 2024
e0bfb75
remove gcloud auth list dont need it
nikellepetrillo Dec 18, 2024
c315176
remove gcloud auth list dont need it
nikellepetrillo Dec 18, 2024
851ad18
remove gcloud auth list dont need it
nikellepetrillo Dec 18, 2024
f20daab
remove gcloud auth list dont need it
nikellepetrillo Dec 18, 2024
d1346fb
remove gcloud auth list dont need it
nikellepetrillo Dec 18, 2024
9831bdc
remove gcloud auth list dont need it
nikellepetrillo Dec 18, 2024
394cad4
remove gcloud auth list dont need it
nikellepetrillo Dec 18, 2024
af221f6
return method_config_name
nikellepetrillo Dec 18, 2024
99d59fe
return method_config_name
nikellepetrillo Dec 18, 2024
5fa1fc4
return method_config_name
nikellepetrillo Dec 18, 2024
84990fb
return method_config_name
nikellepetrillo Dec 19, 2024
2a1ae5f
return method_config_name
nikellepetrillo Dec 19, 2024
c8bec3f
return method_config_name
nikellepetrillo Dec 19, 2024
66a1b14
return method_config_name
nikellepetrillo Dec 19, 2024
961f199
cat github env
nikellepetrillo Dec 19, 2024
8bfb62e
cat github env
nikellepetrillo Dec 19, 2024
0fa7861
cat github env
nikellepetrillo Dec 19, 2024
159f4b1
cat github env
nikellepetrillo Dec 19, 2024
d4de136
cat github env
nikellepetrillo Dec 19, 2024
ea4603f
cat github env
nikellepetrillo Dec 19, 2024
f68ef5c
cat github env
nikellepetrillo Dec 19, 2024
830d8bb
cat github env
nikellepetrillo Dec 19, 2024
4164ceb
cat github env
nikellepetrillo Dec 19, 2024
ae7d1e8
cat github env
nikellepetrillo Dec 19, 2024
f7cb219
cat github env
nikellepetrillo Dec 19, 2024
3a3c136
cat github env
nikellepetrillo Dec 19, 2024
13bd768
cat github env
nikellepetrillo Dec 19, 2024
d5c9d2d
cat github env
nikellepetrillo Dec 19, 2024
66f5101
cat github env
nikellepetrillo Dec 19, 2024
f8650b4
cat github env
nikellepetrillo Dec 19, 2024
993abe8
cat github env
nikellepetrillo Dec 19, 2024
ef0888b
cat github env
nikellepetrillo Dec 19, 2024
47e6298
cat github env
nikellepetrillo Dec 19, 2024
f1d4b25
cat github env
nikellepetrillo Dec 19, 2024
59ed7ab
cat github env
nikellepetrillo Dec 19, 2024
a7d9330
cat github env
nikellepetrillo Dec 20, 2024
b4cf988
clean up
nikellepetrillo Dec 20, 2024
9f5ffb5
clean up
nikellepetrillo Dec 20, 2024
9c6b835
more clean up
nikellepetrillo Dec 20, 2024
9f1ee64
more clean up
nikellepetrillo Dec 20, 2024
e007277
more clean up
nikellepetrillo Dec 20, 2024
ccbaa68
more clean up
nikellepetrillo Dec 20, 2024
024cbdf
more clean up
nikellepetrillo Dec 20, 2024
8bc1623
more clean up
nikellepetrillo Dec 20, 2024
dc9e046
more clean up
nikellepetrillo Dec 20, 2024
640cca8
more clean up
nikellepetrillo Dec 20, 2024
a76ca3b
more clean up
nikellepetrillo Dec 20, 2024
9ef54c1
trying to port optimus for fun!!
nikellepetrillo Dec 20, 2024
51c019d
trying to port optimus for fun!!
nikellepetrillo Dec 20, 2024
ab16c5a
trying to port optimus for fun!!
nikellepetrillo Dec 20, 2024
df24e66
trying to port optimus for fun!!
nikellepetrillo Dec 20, 2024
06ff6c1
update UpdateTestInputs.py to handle array inputs
nikellepetrillo Dec 20, 2024
10f2358
update UpdateTestInputs.py to handle array inputs
nikellepetrillo Dec 20, 2024
851ea2c
update UpdateTestInputs.py to handle array inputs
nikellepetrillo Dec 20, 2024
d2177d2
fix branch name
nikellepetrillo Dec 20, 2024
611f615
fix branch name
nikellepetrillo Dec 20, 2024
f6999c7
fix branch name
nikellepetrillo Dec 20, 2024
ffc35a1
fix branch name
nikellepetrillo Dec 20, 2024
91e5e08
fix branch name
nikellepetrillo Dec 20, 2024
71c6f13
try updating test inputs again
nikellepetrillo Dec 20, 2024
8ed871b
try updating test inputs again
nikellepetrillo Dec 20, 2024
4f0808c
try updating test inputs again
nikellepetrillo Dec 20, 2024
ea7a656
try updating test inputs again
nikellepetrillo Dec 20, 2024
7a0a54b
try updating test inputs again
nikellepetrillo Dec 20, 2024
e835494
try updating test inputs again
nikellepetrillo Dec 20, 2024
a43087b
fix setting the test type
nikellepetrillo Dec 20, 2024
55dfd64
fix setting the test type
nikellepetrillo Dec 20, 2024
b38e333
fix setting the test type
nikellepetrillo Dec 20, 2024
1129af4
fix setting the test type
nikellepetrillo Dec 20, 2024
5baa80f
fix setting the test type
nikellepetrillo Dec 21, 2024
83561b1
fix setting the test type
nikellepetrillo Dec 21, 2024
923cddf
fix the quote values function
nikellepetrillo Dec 21, 2024
5daa964
fix the quote values function
nikellepetrillo Dec 21, 2024
b5d5938
fix the quote values function
nikellepetrillo Dec 21, 2024
2b47e4a
fix the quote values function
nikellepetrillo Dec 21, 2024
8402280
pushing a commit to trigger
nikellepetrillo Dec 30, 2024
f074702
udate quote values to handle arrays?
nikellepetrillo Dec 30, 2024
a034d79
udate quote values to handle arrays?
nikellepetrillo Dec 30, 2024
2360cd7
make truth path and results path dynamic
nikellepetrillo Dec 30, 2024
c00128f
make pipeline_dir dynamic
nikellepetrillo Dec 30, 2024
c1f90a0
fix submission url
nikellepetrillo Dec 30, 2024
2acbbc3
fix submission url
nikellepetrillo Dec 30, 2024
b6152e0
make both tests the same
nikellepetrillo Jan 2, 2025
ff623f4
make both tests the same
nikellepetrillo Jan 2, 2025
4f05889
add testsnm3c to dockstore yml
nikellepetrillo Jan 2, 2025
853ca7a
port snm3c
nikellepetrillo Jan 2, 2025
391a161
port snm3c
nikellepetrillo Jan 2, 2025
53fa6a2
debugging fetch_dockstore_commit.py
nikellepetrillo Jan 2, 2025
9afb448
debugging fetch_dockstore_commit.py
nikellepetrillo Jan 2, 2025
508f84d
debugging fetch_dockstore_commit.py
nikellepetrillo Jan 2, 2025
86a3a76
debugging fetch_dockstore_commit.py
nikellepetrillo Jan 2, 2025
02475a6
remove nested inputs
nikellepetrillo Jan 2, 2025
d37ade7
remove nested inputs
nikellepetrillo Jan 2, 2025
cce354d
Lk atac test porting (#1457)
ekiernan Jan 2, 2025
ebae52a
try to add testmultiome
nikellepetrillo Jan 2, 2025
efd99f2
Merge remote-tracking branch 'origin/np_jw_test_illumina_genotyping_a…
nikellepetrillo Jan 2, 2025
af3bf20
add variant call test
jessicaway Jan 2, 2025
339e0da
additional changes to add variant calling test
jessicaway Jan 2, 2025
1f69e8b
Merge branch 'develop' into np_jw_test_illumina_genotyping_arrays
nikellepetrillo Jan 3, 2025
d37b6da
add http imports to TestMultiome.wdl and Multiome.wdl
nikellepetrillo Jan 3, 2025
e08b2c4
add TestReblockGVCF.wdl to the new testing framework
nikellepetrillo Jan 3, 2025
fbdfaa5
try to handle stucts
nikellepetrillo Jan 6, 2025
db9c669
try to handle stucts
nikellepetrillo Jan 6, 2025
a40af64
try to handle stucts
nikellepetrillo Jan 6, 2025
9314d93
try to handle stucts
nikellepetrillo Jan 6, 2025
b61ab66
try to handle stucts
nikellepetrillo Jan 6, 2025
ebbba91
try to handle stucts
nikellepetrillo Jan 6, 2025
0723f3d
try to handle stucts
nikellepetrillo Jan 6, 2025
f692d50
handle nested inputs
nikellepetrillo Jan 6, 2025
5fbfd41
handle nested inputs
nikellepetrillo Jan 6, 2025
afe8d0b
Merge branch 'np_jw_test_illumina_genotyping_arrays' into jw_add_vari…
jessicaway Jan 6, 2025
03556b2
add wgs germline ss
nikellepetrillo Jan 7, 2025
1ac056e
try testing with removing always
nikellepetrillo Jan 7, 2025
133e525
Lk add exome testing (#1461)
ekiernan Jan 7, 2025
5ee93d2
try testing with removing always
nikellepetrillo Jan 7, 2025
0f30723
Merge branch 'np_jw_test_illumina_genotyping_arrays' into jw_add_vari…
jessicaway Jan 7, 2025
d09f395
Rc test smartseq 3 (#1466)
rsc3 Jan 7, 2025
0d12069
try testing with removing always
nikellepetrillo Jan 8, 2025
f2fedf0
Merge remote-tracking branch 'origin/np_jw_test_illumina_genotyping_a…
nikellepetrillo Jan 8, 2025
88385ce
add OVERALL_SUCCESS to all tests
nikellepetrillo Jan 8, 2025
4984196
Merge pull request #1464 from broadinstitute/jw_add_variant_calling_test
jessicaway Jan 8, 2025
aadb548
Lk rnawithumis testing (#1467)
ekiernan Jan 8, 2025
34ed9fa
Merge branch 'develop' into np_jw_test_illumina_genotyping_arrays
nikellepetrillo Jan 8, 2025
3b791fc
add OVERALL_SUCCESS to all tests again
nikellepetrillo Jan 8, 2025
7326a84
add OVERALL_SUCCESS to all tests again
nikellepetrillo Jan 8, 2025
e82851e
add joint genotyping
nikellepetrillo Jan 8, 2025
acf467c
add UltimaGenomicsWholeGenomeGermline
nikellepetrillo Jan 8, 2025
8466d33
remove https and move generate file summary after all procesing is co…
nikellepetrillo Jan 9, 2025
ab481f8
fix summary tables for all ymls
nikellepetrillo Jan 9, 2025
8b3e3d5
add testslideseq to dockstore
rsc3 Jan 9, 2025
58502bc
update run_pipeline
nikellepetrillo Jan 10, 2025
f7975ed
update run_pipeline
nikellepetrillo Jan 10, 2025
b163cc8
update run_pipeline
nikellepetrillo Jan 10, 2025
3f4677c
update run_pipeline
nikellepetrillo Jan 10, 2025
bdd9581
update run_pipeline
nikellepetrillo Jan 10, 2025
181dedf
fix slideseq test wdl path
rsc3 Jan 10, 2025
afef2b1
Ultima Whole Genome Cram Only testing (#1472)
ekiernan Jan 10, 2025
d3411cb
try updating usercomment
nikellepetrillo Jan 10, 2025
d4882be
Merge remote-tracking branch 'origin/np_jw_test_illumina_genotyping_a…
nikellepetrillo Jan 10, 2025
4275985
try updating usercomment
nikellepetrillo Jan 10, 2025
72d40bc
try updating usercomment
nikellepetrillo Jan 10, 2025
a9b93ac
try updating usercomment
nikellepetrillo Jan 10, 2025
7872add
try updating usercomment
nikellepetrillo Jan 10, 2025
7e7d9a7
try updating usercomment
nikellepetrillo Jan 10, 2025
9ceefaa
move submission data file
nikellepetrillo Jan 10, 2025
e963159
move submission data file
nikellepetrillo Jan 10, 2025
7eec5cf
move eof
nikellepetrillo Jan 10, 2025
786985f
move eof
nikellepetrillo Jan 10, 2025
370a517
move eof
nikellepetrillo Jan 10, 2025
75456f6
move eof
nikellepetrillo Jan 10, 2025
e7e2487
move eof
nikellepetrillo Jan 10, 2025
4f57314
move eof
nikellepetrillo Jan 10, 2025
d4df51e
move eof
nikellepetrillo Jan 10, 2025
f7e29c7
move eof
nikellepetrillo Jan 10, 2025
53afc37
input_file instead of test_input_file
nikellepetrillo Jan 10, 2025
e2f045e
input_file instead of test_input_file
nikellepetrillo Jan 10, 2025
e9d9504
input_file instead of test_input_file
nikellepetrillo Jan 10, 2025
091fd64
input_file instead of test_input_file
nikellepetrillo Jan 10, 2025
442bce1
start slideseq yml with task wdls
rsc3 Jan 10, 2025
d292e15
update test wdl and yaml
rsc3 Jan 11, 2025
b6ec64f
add input json name to user comment
nikellepetrillo Jan 13, 2025
ca323eb
Updated pipeline_versions.txt with all pipeline version information
actions-user Jan 13, 2025
9aaf24b
add ultima joint genotyping
nikellepetrillo Jan 13, 2025
ed188ad
Merge remote-tracking branch 'origin/np_jw_test_illumina_genotyping_a…
nikellepetrillo Jan 13, 2025
764ee37
add cram to unmapped bams
nikellepetrillo Jan 13, 2025
4fc1e15
fix testslideseq paths
rsc3 Jan 13, 2025
f1266d4
Updated pipeline_versions.txt with all pipeline version information
actions-user Jan 13, 2025
488c1d1
add exomereprocessing
nikellepetrillo Jan 13, 2025
18fcc36
add wholeGenomeReprocessing
nikellepetrillo Jan 13, 2025
153d436
update jobs to TestSlideSeq
rsc3 Jan 14, 2025
dc2e1f8
remove truth_branch and replace with master
nikellepetrillo Jan 14, 2025
defb52f
test out adding authorized_users.yml
nikellepetrillo Jan 14, 2025
ab472c7
test out adding authorized_users.yml
nikellepetrillo Jan 14, 2025
6862a01
test out adding authorized_users.yml
nikellepetrillo Jan 14, 2025
4fb1fe8
test out adding authorized_users.yml
nikellepetrillo Jan 14, 2025
9836e10
update post
nikellepetrillo Jan 14, 2025
f8abc45
update post
nikellepetrillo Jan 14, 2025
74aa95f
update post
nikellepetrillo Jan 14, 2025
aed7a20
update post
nikellepetrillo Jan 14, 2025
3ff185b
echo reponse
nikellepetrillo Jan 14, 2025
be2f90a
use np_jw_test_illumina_genotyping_arrays
nikellepetrillo Jan 14, 2025
5750521
use np_jw_test_illumina_genotyping_arrays
nikellepetrillo Jan 14, 2025
9026b01
make testType not required
nikellepetrillo Jan 14, 2025
d9425cb
make testType not required
nikellepetrillo Jan 14, 2025
7cd07ca
make testType not required
nikellepetrillo Jan 14, 2025
e0ef135
make testType not required
nikellepetrillo Jan 14, 2025
0fb694e
make testType not required
nikellepetrillo Jan 14, 2025
6db467d
make testType not required
nikellepetrillo Jan 14, 2025
bcb5fb2
make testType not required
nikellepetrillo Jan 14, 2025
6afef86
make testType not required
nikellepetrillo Jan 14, 2025
46e64bb
restructure how we check authed users
nikellepetrillo Jan 14, 2025
e839b9b
restructure how we check authed users
nikellepetrillo Jan 14, 2025
8939dbc
restructure how we check authed users
nikellepetrillo Jan 14, 2025
ce785a1
restructure how we check authed users
nikellepetrillo Jan 14, 2025
17c8e78
restructure how we check authed users
nikellepetrillo Jan 14, 2025
bb106e6
restructure how we check authed users
nikellepetrillo Jan 14, 2025
2307de1
restructure how we check authed users
nikellepetrillo Jan 14, 2025
71b8672
restructure how we check authed users
nikellepetrillo Jan 14, 2025
35492e0
restructure how we check authed users
nikellepetrillo Jan 14, 2025
6ed23ea
restructure how we check authed users
nikellepetrillo Jan 14, 2025
8c688c5
Merge branch 'develop' into np_jw_test_illumina_genotyping_arrays
nikellepetrillo Jan 15, 2025
e0a9cec
test out cram to ubam
nikellepetrillo Jan 16, 2025
6371018
dont convert float to scientific notation
nikellepetrillo Jan 16, 2025
4a9beef
Merge branch 'np_jw_test_illumina_genotyping_arrays' into rc_test_sli…
nikellepetrillo Jan 17, 2025
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5 changes: 3 additions & 2 deletions .github/workflows/authorized_users.yml
Original file line number Diff line number Diff line change
@@ -50,7 +50,8 @@ jobs:
-d '{
"ref": "np_jw_test_illumina_genotyping_arrays",
"inputs": {
"testType": "Plumbing"
}
}'
# Check the response
echo "Response: $?"
#echo repsonse
echo "Response: $response"