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Rc peakcall 2797 #1478

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merged 111 commits into from
Feb 5, 2025
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ce90d53
add peak calling
aawdeh Oct 16, 2024
82c5c45
added output for peaks
aawdeh Oct 16, 2024
6e833d2
fix
aawdeh Oct 16, 2024
76286b4
fix
aawdeh Oct 16, 2024
90805ca
test
aawdeh Oct 16, 2024
b27011c
remove ls
aawdeh Oct 17, 2024
c1f0e57
test
aawdeh Oct 18, 2024
90b193c
Merge branch 'develop' into aa-peakcall
aawdeh Oct 18, 2024
779fe9b
test
aawdeh Oct 18, 2024
6d52ad2
Merge branch 'aa-peakcall' of https://github.com/broadinstitute/warp …
aawdeh Oct 18, 2024
5743eff
test
aawdeh Oct 18, 2024
d3749c8
test
aawdeh Oct 18, 2024
1de1c85
test
aawdeh Oct 18, 2024
2d18756
test
aawdeh Oct 18, 2024
13a44f9
test
aawdeh Oct 21, 2024
3f12b9e
made another task
aawdeh Oct 21, 2024
08b2f24
test
aawdeh Oct 21, 2024
80c1416
test
aawdeh Oct 21, 2024
b5191e5
test
aawdeh Oct 21, 2024
4725080
test
aawdeh Oct 21, 2024
f139f84
test
aawdeh Oct 22, 2024
9a0ea9b
test
aawdeh Oct 22, 2024
04cf0d2
test
aawdeh Oct 22, 2024
f9bc871
change a line
aawdeh Oct 24, 2024
93d3360
test
aawdeh Oct 24, 2024
256c4e5
test
aawdeh Oct 24, 2024
cd849b5
test
aawdeh Oct 24, 2024
7c62fd1
test
aawdeh Oct 24, 2024
b15b146
test
aawdeh Oct 24, 2024
ff36c15
test
aawdeh Oct 24, 2024
27a4196
test
aawdeh Oct 24, 2024
987b5d2
Add peakcall to task
aawdeh Oct 28, 2024
cce5841
test
aawdeh Oct 28, 2024
39ef1a5
Merge branch 'develop' into aa-peakcall
aawdeh Oct 28, 2024
bf0e9ce
add parameters
aawdeh Oct 28, 2024
d9240d6
Merge branch 'aa-peakcall' of https://github.com/broadinstitute/warp …
aawdeh Oct 28, 2024
1ec5ff1
Merge branch 'develop' into aa-peakcall
aawdeh Oct 30, 2024
90172ee
Merge branch 'develop' into aa-peakcall
aawdeh Nov 4, 2024
18f77d8
test
aawdeh Nov 4, 2024
f7bdfa2
Merge branch 'aa-peakcall' of https://github.com/broadinstitute/warp …
aawdeh Nov 4, 2024
db59231
peak calling
rsc3 Dec 13, 2024
7b5a87e
looking for conflicts in atac.wdl
rsc3 Dec 13, 2024
0d4f010
remove bam_base_name from CreateFragments task
rsc3 Dec 13, 2024
987e1e5
separate task for macs3 consistent with create fragments
rsc3 Dec 13, 2024
0bc38f6
Update atac.wdl
rsc3 Dec 16, 2024
b136ba3
snapatac2 updates
rsc3 Dec 16, 2024
573a29f
turn off createfragments peakcalling
rsc3 Jan 13, 2025
7b8d1fc
remove peakcalling from createfragments and parameterize probability_…
rsc3 Jan 14, 2025
0689868
remove probability_threshold parameterization
rsc3 Jan 14, 2025
32f4b7f
remove repeated line
rsc3 Jan 14, 2025
fffb256
Updated pipeline_versions.txt with all pipeline version information
actions-user Jan 14, 2025
cf2a77b
add optional parameter
aawdeh Jan 19, 2025
41de09c
Merge branch 'develop' into rc_peakcall_2797
aawdeh Jan 19, 2025
cf63ad1
add output
aawdeh Jan 21, 2025
093faea
Merge branch 'rc_peakcall_2797' of https://github.com/broadinstitute/…
aawdeh Jan 21, 2025
5e81613
add output
aawdeh Jan 21, 2025
f0216ab
test
aawdeh Jan 21, 2025
ef09ec9
test
aawdeh Jan 21, 2025
d64ad4d
test
aawdeh Jan 21, 2025
e3fe25f
test
aawdeh Jan 21, 2025
e6dad58
test
aawdeh Jan 21, 2025
dd9c77b
Merge branch 'develop' into rc_peakcall_2797
aawdeh Jan 21, 2025
80e3fa1
Added matrix as output
aawdeh Jan 27, 2025
75e8f2f
Merge branch 'rc_peakcall_2797' of https://github.com/broadinstitute/…
aawdeh Jan 27, 2025
b3ebae9
Updated pipeline_versions.txt with all pipeline version information
actions-user Jan 27, 2025
9e4916a
Added matrix as output
aawdeh Jan 27, 2025
13a448a
Merge branch 'rc_peakcall_2797' of https://github.com/broadinstitute/…
aawdeh Jan 27, 2025
cd7c100
Added matrix as output
aawdeh Jan 27, 2025
d7486d9
test
aawdeh Jan 28, 2025
89824b0
test
aawdeh Jan 28, 2025
aee56ec
remove comments
aawdeh Jan 28, 2025
f90905b
Merge branch 'develop' into rc_peakcall_2797
aawdeh Jan 31, 2025
83fbe05
update changelogs/versions
aawdeh Jan 31, 2025
af76a98
Merge branch 'rc_peakcall_2797' of https://github.com/broadinstitute/…
aawdeh Jan 31, 2025
a0dd316
Updated pipeline_versions.txt with all pipeline version information
actions-user Jan 31, 2025
5680637
documenation
aawdeh Jan 31, 2025
f53e592
Merge branch 'rc_peakcall_2797' of https://github.com/broadinstitute/…
aawdeh Jan 31, 2025
745d9c4
rename
aawdeh Jan 31, 2025
54694bc
rename
aawdeh Jan 31, 2025
c664618
rename
aawdeh Jan 31, 2025
328ec9a
rename
aawdeh Jan 31, 2025
3ee54aa
fix
aawdeh Feb 3, 2025
a3e99ce
fix
aawdeh Feb 3, 2025
eaa28d6
Merge branch 'develop' into rc_peakcall_2797
aawdeh Feb 3, 2025
581d039
fix
aawdeh Feb 3, 2025
7a9dd2d
Merge branch 'rc_peakcall_2797' of https://github.com/broadinstitute/…
aawdeh Feb 3, 2025
b5f0d2f
fix
aawdeh Feb 3, 2025
9ca0202
fix
aawdeh Feb 3, 2025
d7b84de
fix
aawdeh Feb 3, 2025
e699564
add peak call json
aawdeh Feb 3, 2025
0159899
fix
aawdeh Feb 3, 2025
6d95b96
fix
aawdeh Feb 3, 2025
c2e4649
Updated pipeline_versions.txt with all pipeline version information
actions-user Feb 3, 2025
9dd8e2a
fix
aawdeh Feb 3, 2025
8e1480d
Merge branch 'rc_peakcall_2797' of https://github.com/broadinstitute/…
aawdeh Feb 3, 2025
89189c0
fix
aawdeh Feb 3, 2025
86bee87
fix
aawdeh Feb 3, 2025
d2a77e7
fix
aawdeh Feb 3, 2025
15950ec
Updated pipeline_versions.txt with all pipeline version information
actions-user Feb 3, 2025
049af9d
fix
aawdeh Feb 3, 2025
b9a1a60
Merge branch 'rc_peakcall_2797' of https://github.com/broadinstitute/…
aawdeh Feb 3, 2025
1a02ba7
fix
aawdeh Feb 3, 2025
ba0982a
updating TestMultiome to run peak calling
ekiernan Feb 3, 2025
1023faa
update expected_cells and parameterize probability thresholds
rsc3 Feb 3, 2025
09adf51
expected cells as integer
rsc3 Feb 3, 2025
2681b75
fix
aawdeh Feb 4, 2025
6a5f83f
update probability_threshold
rsc3 Feb 4, 2025
e1cdc14
remove quotes around probability_threshold
rsc3 Feb 4, 2025
92468ef
remove typo
rsc3 Feb 4, 2025
6bca8f5
fix
aawdeh Feb 4, 2025
01249c2
fix
aawdeh Feb 4, 2025
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Merge branch 'develop' into rc_peakcall_2797
aawdeh authored Jan 31, 2025
commit f90905b326c190f9695c927017321facc462a760

This merge commit was added into this branch cleanly.

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