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Arcadia-Science
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noveltree
NovelTree is a highly parallelized and computationally efficient phylogenomic workflow that infers gene families, gene family trees, species trees, and gene family evolutionary history.
GNU Affero General Public License v3.0
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Ap/spp tree prep fix
#53
austinhpatton
closed
1 year ago
0
Ap/speciesrax fix
#52
austinhpatton
closed
1 year ago
0
Add example of memory/cpu specification to quickstart of readme
#51
austinhpatton
closed
1 year ago
0
Process specification/optimization
#50
austinhpatton
closed
1 year ago
1
Ap/parallel annotation
#49
austinhpatton
closed
1 year ago
0
Added noninteractive ENV back into images
#48
austinhpatton
closed
1 year ago
0
Ap/iqtree docker
#47
austinhpatton
closed
1 year ago
0
speciesrax/generax fix for excluded gene families
#46
austinhpatton
closed
1 year ago
0
Ap/cogeqc fix
#45
austinhpatton
closed
1 year ago
0
Use GitHub actions to build and publish Docker images
#44
mertcelebi
opened
1 year ago
0
Update Docker base images and optimize size
#43
mertcelebi
opened
1 year ago
0
License -> AGPL-3
#42
austinhpatton
closed
1 year ago
0
Ap/workflow fig readme
#41
austinhpatton
closed
1 year ago
1
DockerFiles
#40
mertcelebi
closed
1 year ago
0
Prioritize MSAs for gene families used in species tree inference
#39
austinhpatton
closed
1 year ago
2
Use minimal set of annotations for COGEQC orthogroup QC
#38
austinhpatton
closed
1 year ago
0
Only run busco if dataset != NA
#37
austinhpatton
closed
1 year ago
5
Description of nf-core modifications and inclusion of nf-core git-shas
#36
austinhpatton
closed
1 year ago
3
Update CITATIONS.md
#35
austinhpatton
closed
1 year ago
1
Ap/bash variables
#34
austinhpatton
closed
1 year ago
1
Code clean-up part deux
#33
mertcelebi
closed
1 year ago
0
Ap/readme outputs
#32
austinhpatton
closed
1 year ago
1
Code cleanup part #1
#31
mertcelebi
closed
1 year ago
0
Ap/parameterization
#30
austinhpatton
closed
1 year ago
2
Ap/biological test dataset
#29
mertcelebi
closed
1 year ago
0
Fixes mpi thread specification in asteroid, generax and speciesrax
#28
austinhpatton
closed
1 year ago
0
Parameterizing software inputs
#27
austinhpatton
closed
1 year ago
0
Handling of compressed inputs
#26
austinhpatton
opened
1 year ago
0
Remove test data and update the README
#25
mertcelebi
closed
1 year ago
0
Update the schema file
#24
mertcelebi
closed
1 year ago
0
Fix more hardcoded paths
#23
mertcelebi
closed
1 year ago
0
Make bin/ scripts executable and fix their invocations
#22
mertcelebi
closed
1 year ago
1
Monophyly constraints for gene tree and/or species tree inference
#21
austinhpatton
closed
1 year ago
0
Fix species tree root at TMRCA of Eukaryotes and Archaea
#20
austinhpatton
closed
1 year ago
0
Use stubs for testing
#19
mertcelebi
closed
1 year ago
1
README overhaul
#18
mertcelebi
closed
1 year ago
0
Add Dockerfiles that Austin created to the actual repo
#17
mertcelebi
closed
1 year ago
0
Clean-up INPUT_CHECK to make sure meta fields are useful
#16
mertcelebi
closed
1 year ago
1
Move the test files to Arcadia's test data repo
#15
mertcelebi
closed
1 year ago
0
Simplify the branching logic after inflation selection
#14
mertcelebi
closed
1 year ago
0
Remove unused def args = task.ext.args ?: ' from processes.
#13
mertcelebi
closed
1 year ago
0
Making the names of bash script variables consistent
#12
mertcelebi
closed
1 year ago
0
Make sure the email notifications work and the code compiles
#11
mertcelebi
closed
1 year ago
0
Clean-up config files
#10
mertcelebi
closed
1 year ago
0
Using subworkflows more to clean-up the mcl_test vs complete separation.
#9
mertcelebi
opened
1 year ago
0
Validation of input species counts and more meaningful error messages
#8
mertcelebi
opened
1 year ago
0
This fixes all the issues related to S3 staging and the usage of hard-coded paths
#7
mertcelebi
closed
1 year ago
1
Parsing into HOGs
#6
austinhpatton
closed
1 year ago
0
Use subworkflows more to reduce the amount of duplicate imports in the main workflow
#5
mertcelebi
closed
1 year ago
1
Create module to get HOGs
#4
austinhpatton
closed
1 year ago
0
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