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Merged
merged 55 commits into from
May 19, 2025
Merged

Conversion from GCP to AWS complete #17

merged 55 commits into from
May 19, 2025

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aolveraNIH
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Pull Request Template

Description

Converted from TransPi to nf-core denovotranscrip pipeline workflow and converted from GCP to AWS.

Assignee

*Assignees: @kyleoconnell-NIH and/or @jpinney32 *

PR checklist

Please ensure the following:

  • This comment contains a description of changes (with reason).
  • All changes were tested.
  • If you've fixed a bug mention the issue number/name.
  • Apply approriate tags (e.g. documentation, bug)

hadiparsianNIH and others added 30 commits January 14, 2025 13:43
@hadiparsianNIH
Created AWS-GCP
7efe657
@hadiparsianNIH
Changed the format of submodule 00
e221614
Github Action: Lint Notebooks
42dd2e9
@hadiparsianNIH
fixed the typo in submodule 00
2dd6da9
@hadiparsianNIH
changed the format of the GCP
912ea24
Github Action: Lint Notebooks
9cf17a1
@hadiparsianNIH
Created AWS folder
ac69cf2
@hadiparsianNIH
modified README
a9fe503
@hadiparsianNIH
updated README in the main part
c23d61e
@hadiparsianNIH
Added modules from gcp to AWS
f702a5b
@hadiparsianNIH
corrected typo in submoduloe1 GCP
c20fba6
Github Action: Lint Notebooks
f423386
@hadiparsianNIH
moved quiz to the main folder
1deb650
Github Action: Lint Notebooks
ebe56e9
@hadiparsianNIH
updated submodule 00 and 01 in AWS
29aada2
Github Action: Lint Notebooks
dd05bbf
@aolveraNIH
denovo nf-core pipeline is running, working on adding google batch
2a9d943
@aolveraNIH
denovo nf-core pipeline is running, working on adding google batch
8cee886
@aolveraNIH
Updated outdir and workDir with placeholder variables
d0b8c9d
@aolveraNIH
Added steps for renaming bucket
a26c96b
Github Action: Lint Notebooks
e1e326e
@aolveraNIH
Added missing -i in sed command
b172a4d
@aolveraNIH
Merge branch 'denovo_nf-core' of https://github.com/NIGMS/Transcripto…
d94bbdc 
…me-Assembly-Refinement-and-Applications into denovo_nf-core

fixed merge conflict due to not setting branch
@aolveraNIH
Added nextflow command line
0b09e9f
@hadiparsianNIH
moved all the images into one directory
94ece16
@hadiparsianNIH
modified aws directory
18d0854
@hadiparsianNIH
corrected images path
21a4638
@hadiparsianNIH
moved "denovotrascript" to the main directory
2c649ad
@hadiparsianNIH
Renamed submodules to reorder them
c67e64d
Github Action: Lint Notebooks
a61ef58
aolveraNIH and others added 22 commits May 2, 2025 13:26
@aolveraNIH
Fixed bugs in denovotranscript.nf and nextflow.config files. Fixed so…
5ed3035 
…me of the commands in submodule 2
@aolveraNIH
fixed BUSCO part to run on GCP
551ab8f
@aolveraNIH
Updated last part of busco analysis
3c9dbaa
@jghanaim04
Create README.md shell for AWS folder
fc699b3
@jghanaim04
Create README.md shell for GoogleCloud folder
c41c7b2
@aolveraNIH
Updated nextflow command to run with files in denovotranscript folder
0181be9
@jghanaim04
Update README.md
6bbddb2 
Updated README to be AWS-specific but left a couple parts highlighted that still require updates
@jghanaim04
Update README.md
21d80f5 
Updated README to be GCP-specific
@aolveraNIH
Finished updating submodule 3 readme
c48549c
@jghanaim04
Update README.md
8b27c66 
Updated README to be AWS-specific - still requires some changes highlighted
@aolveraNIH
Added in learning objectives and conclusion
d0e188d
@jghanaim04
Update README.md
69a896a 
Fixed images and removed funding info
@jghanaim04
Update README.md
430b7c0 
Updated bucket from GCP to AWS
@jghanaim04
Removed references to switching kernels, updated nextflow command to …
8e04ff2 
…run with files in denovotranscript folder, and other minor cleanup
@jghanaim04
Update README.md
90118c1 
Generalized for AWS/GCP
@jghanaim04
Update README.md
8088a41 
Updated troubleshooting section
@jghanaim04
Update README.md
d66de74 
Updated troubleshooting section
@aolveraNIH
Updated
2032c3a
@aolveraNIH
Merge branch 'rebased_denovo_nf-core' into AWS-GCP
7d15876 
Merging rebased denovo nf-core branch to AWS-GCP branch
@aolveraNIH
Updated diagram of workflow
37a1310
@aolveraNIH
Updated workflow diagrams within platform specific folders to archite…
c819238 
…cture diagrams
@aolveraNIH
Updated workflow diagrams within platform specific folders to archite…
2ea68b6 
…cture diagrams
@aolveraNIH aolveraNIH added the enhancement New feature or request label May 14, 2025
@kyleoconnell-NIH kyleoconnell-NIH merged commit 346a552 into master May 19, 2025
1 of 3 checks passed
@kyleoconnell-NIH kyleoconnell-NIH deleted the AWS-GCP branch May 19, 2025 17:57
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Reviewers

@kyleoconnell-NIH kyleoconnell-NIH kyleoconnell-NIH approved these changes

@jpinney32 jpinney32 Awaiting requested review from jpinney32

Assignees

@jpinney32 jpinney32

@kyleoconnell-NIH kyleoconnell-NIH

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5 participants

@aolveraNIH @kyleoconnell-NIH @jpinney32 @hadiparsianNIH @jghanaim04