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Lk pd 2736 doublets #1362

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merged 38 commits into from
Oct 2, 2024
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3af3631
adding cell calls as output of merge star outputs for calling cells
ekiernan Aug 20, 2024
0b3ad39
fixing syntax
ekiernan Aug 20, 2024
1495864
updated h5ad utils to include new warp-tools script for doublets
ekiernan Aug 21, 2024
8d3fec6
added test docker to Optimus
ekiernan Aug 21, 2024
df26128
fixed womtools
ekiernan Aug 21, 2024
9e4e14f
fixed docker name
ekiernan Aug 21, 2024
fec3ebc
testing new dockers for star-merge-npz and warp-tools to allow keeper…
ekiernan Aug 22, 2024
4067ecc
adding quotes around gex_nhash_id because it is null
ekiernan Aug 27, 2024
0440776
Merge branch 'develop' into lk-PD-2736-doublets
ekiernan Sep 18, 2024
4499866
Updated pipeline_versions.txt with all pipeline version information
actions-user Sep 18, 2024
66d8f89
updated documentation
ekiernan Sep 20, 2024
f133e90
Updated pipeline_versions.txt with all pipeline version information
actions-user Sep 21, 2024
338b886
setting null for multiome
ekiernan Sep 21, 2024
b56656c
Merge branch 'lk-PD-2736-doublets' of https://github.com/broadinstitu…
ekiernan Sep 21, 2024
d1dd9f7
typo
ekiernan Sep 21, 2024
86e3a21
added select first to library metrics
ekiernan Sep 23, 2024
289b3a3
fixing broken link in doc test
ekiernan Sep 23, 2024
dac4de4
nhash_id optional
ekiernan Sep 23, 2024
a8539f5
updating syntax for add_library_tso_doublets
ekiernan Sep 23, 2024
6e1ed35
Update H5adUtils.wdl
ekiernan Sep 23, 2024
278ad86
fix brace
ekiernan Sep 23, 2024
f691fbd
adding bash for optional nhash
ekiernan Sep 23, 2024
5e84c07
updated selectfirst for optimus task
ekiernan Sep 23, 2024
c88419b
fixed rbrace
ekiernan Sep 23, 2024
80a07d6
small change
ekiernan Sep 23, 2024
f6b50b7
reverting select_first
ekiernan Sep 23, 2024
30752a5
adding official docker image tags
ekiernan Sep 24, 2024
3616a3d
Merge branch 'develop' into lk-PD-2736-doublets
ekiernan Sep 24, 2024
5235755
added gex and atac nhash_id to Multiome and paired-tag
ekiernan Sep 24, 2024
01930c9
Merge branch 'lk-PD-2736-doublets' of https://github.com/broadinstitu…
ekiernan Sep 24, 2024
5b380ae
changelog updates
ekiernan Sep 24, 2024
85384f5
Updated pipeline_versions.txt with all pipeline version information
actions-user Sep 24, 2024
5a98363
updating warp-tools and star merge npz dockers on slideseq
ekiernan Sep 24, 2024
0542a61
added expected_cells as input to h5adUtils
ekiernan Sep 26, 2024
61e7597
Merge branch 'develop' into lk-PD-2736-doublets
ekiernan Sep 26, 2024
5329e1a
Updated changelogs
ekiernan Sep 30, 2024
2d31525
Updated readmes for pipeline versions
ekiernan Sep 30, 2024
4d6ce44
updated verify h5ad gex task
ekiernan Oct 2, 2024
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fixed rbrace
  • Loading branch information
ekiernan committed Sep 23, 2024
commit c88419bec68ee8d8af35fc4ea6aa212cfcad3c29
1 change: 1 addition & 0 deletions tasks/skylab/H5adUtils.wdl
Original file line number Diff line number Diff line change
@@ -121,6 +121,7 @@ task OptimusH5adGeneration {
output {
File h5ad_output = "~{input_id}.h5ad"
File library_metrics = select_first(["~{input_id}_~{gex_nhash_id}_gex_library_metrics.csv", "~{input_id}_gex_library_metrics.csv"])
}
}