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Smw tbprofiler continuing dev #199

Merged
merged 37 commits into from
Sep 29, 2023
Merged

Smw tbprofiler continuing dev #199

merged 37 commits into from
Sep 29, 2023

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sage-wright
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Closes

🛠️ Changes Being Made

🧠 Context and Rationale

📋 Workflow/Task Steps

Inputs

Outputs

🧪 Testing

Locally

Terra

🔬 Quality checks

Pull Request (PR) checklist:

  • Include a description of what is in this pull request in this message.
  • The workflow/task has been tested locally and on Terra
  • The CI/CD has been adjusted and tests are passing
  • Everything follows the style guide

sage-wright and others added 30 commits September 11, 2023 20:17
@sage-wright
add to theiaprok
b0c2a0e
@cimendes
add root
5c769b6
@sage-wright
update docker, add spaces
cc2d611
@sage-wright
update docker
a743fef
@sage-wright
update container
0065d25
@sage-wright
update docker
2f9e80a
@aofarrel
Add preemptible, shorter version string (#185)
5227d77
@sage-wright
update docker
8fcfefa
@sage-wright
update docker
7d00801
@sage-wright
update docker
51ddccd
@frankambrosio3
Added clockwork task to theiaprok illumina pe
c924d88
@frankambrosio3
64gb ram
2c5fee9
@cimendes
remove sam file at the end
9d4235e
@frankambrosio3
v8
d617a9f
@frankambrosio3
Merge branch 'smw-tbprofiler-dev' into im-fja-tb-clockwork
304d6ba
@sage-wright
update docker
ac4fd39
@sage-wright
apply style guidelines
c84ce51
@sage-wright
apply style guidelines
7c1a4f1
@cimendes
update md5sum
759180c
@cimendes
only run clockwork is paired_end and not ont data
57e3ef6
@cimendes
try fix
751621b
@sage-wright
update docker
e279d1d
@cimendes
add potential fix for the select_first null issue
d5cd4c7
@cimendes
Merge branch 'im-fja-tb-clockwork' of https://github.com/theiagen/pub…
9ddfabb 
…lic_health_bioinformatics into im-fja-tb-clockwork
@cimendes
update md5sum
74d11fd
@sage-wright
update docker
1318a42
@sage-wright
update docker
d2a6237
@sage-wright
update docker
cf3002d
@sage-wright
update docker
16bd383
@sage-wright
update docker
8d0b72a
sage-wright and others added 4 commits September 26, 2023 19:38
@sage-wright
update docker
a3160b2
@sage-wright
udpate docker
847fa92
@cimendes
TBDB with varpipe (#197)
e8093cd 
* add optional input with alternative input database (set to true by default)

* fix $TBDB call on tb-profiler profile

* wrap optional tbprofiler_custom_db; expose on theiaprok

* update task
@sage-wright
database update
b470601
cimendes
cimendes previously approved these changes Sep 29, 2023
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@kapsakcj
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great work ⭐

@kapsakcj kapsakcj merged commit 34cec39 into main Sep 29, 2023
9 checks passed
@sage-wright sage-wright deleted the smw-tbprofiler-continuing-dev branch October 11, 2023 14:34
@sage-wright sage-wright restored the smw-tbprofiler-continuing-dev branch October 11, 2023 14:34
@sage-wright sage-wright deleted the smw-tbprofiler-continuing-dev branch October 11, 2023 14:50
@sage-wright sage-wright restored the smw-tbprofiler-continuing-dev branch October 11, 2023 14:50
@sage-wright sage-wright deleted the smw-tbprofiler-continuing-dev branch October 24, 2023 14:51
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@kapsakcj kapsakcj kapsakcj approved these changes

@cimendes cimendes cimendes left review comments

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5 participants
@sage-wright @kapsakcj @cimendes @aofarrel @frankambrosio3