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Arcadia-Science
/
prehgt
A pipeline for lightweight screening of Eukaryotic genomes and transcriptomes for recent HGT
MIT License
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Process requirement exceeds available CPUs
#60
onbio
opened
22 hours ago
7
error exit status 2
#59
lagphase
opened
1 month ago
6
converting the `download/*_genome.csv` files into a species list
#58
taylorreiter
opened
4 months ago
0
Download issues with the 2023-nr-clustering sqlite file
#57
Mohammed-Quraishi
closed
4 months ago
3
Bacterial Genera
#56
Nimshika
opened
9 months ago
6
Update Snakemake to parity with Nextflow
#55
lebovic
closed
9 months ago
0
fixing delete_gca_files
#54
giacomomutti
closed
10 months ago
0
Missing corrected bitscores
#53
harrychown
closed
10 months ago
2
Genomes from other than genbank/ncbi
#52
Nimshika
opened
1 year ago
7
Exit gracefully from subkingdom HGT prediction when there are not candidate transfer events
#51
taylorreiter
closed
1 year ago
0
Quick PR to increase ram for frequent failers
#50
taylorreiter
closed
1 year ago
1
Quick PR to add pub DOI to readme
#49
taylorreiter
closed
1 year ago
0
debugging the snakefile so it runs correctly and produces the same outputs as nextflow
#48
taylorreiter
closed
1 year ago
0
swap out R url downloads for copies of files in github repo
#47
taylorreiter
opened
1 year ago
0
Add a step to combine all of the results into one file
#46
taylorreiter
closed
1 year ago
0
Quick PR to change name of process_blast to process_high_cpu
#45
taylorreiter
closed
1 year ago
0
Quick PR to swap out the ncbi genome docker etc with installation from conda
#44
taylorreiter
closed
1 year ago
0
ncbi genome download conda package was patched, so change out from custom docker to conda etc
#43
taylorreiter
closed
1 year ago
0
dockerize & towerize the workflow to enable run on tower
#42
taylorreiter
closed
1 year ago
0
Exit 1 error handling for ncbi-genome-download when exit 1 is expected (for real)
#41
taylorreiter
closed
1 year ago
0
Exit 1 error handling for ncbi-genome-download when exit 1 is expected
#40
taylorreiter
closed
1 year ago
1
change ahs to chs
#39
taylorreiter
closed
1 year ago
0
over time, develop filtering heuristics to systematically remove false positives that repeatedly crop up
#38
taylorreiter
opened
1 year ago
0
Enable CI and fix failures
#37
taylorreiter
opened
1 year ago
1
Documentation PR!
#36
taylorreiter
closed
1 year ago
0
Quick PR to rename the tool to preHGT (prehgt)
#35
taylorreiter
closed
1 year ago
0
Implement a sub-kingdom detection approach via HGTFinder algorithms
#34
taylorreiter
closed
1 year ago
0
`process_blast` is a confusing name. Rename it to something that remarks on the compute usage
#33
taylorreiter
closed
1 year ago
1
Update labels for BLAST results
#32
taylorreiter
closed
1 year ago
0
document nextflow tower execution with wave
#30
taylorreiter
closed
1 year ago
1
deal with email templating in nextflow
#29
taylorreiter
opened
1 year ago
0
Implement a modified aggregate hit score
#28
taylorreiter
closed
1 year ago
0
Add new specificity indices
#27
taylorreiter
closed
1 year ago
0
Change RAAU filtering threshold
#26
taylorreiter
closed
1 year ago
0
Replace EggNog ortholog annotation with kofamscan
#25
taylorreiter
closed
1 year ago
0
Bring in nextflow files from 2023-rehgt-nextflow
#24
taylorreiter
closed
1 year ago
1
think about adding comments to `col_types` strings in R code
#23
taylorreiter
closed
1 year ago
1
consider adding user input of kingdom/NCBI taxonomy set for each genera
#22
taylorreiter
opened
1 year ago
0
implement sub-kingdom math from HGTphyloDetect
#21
taylorreiter
opened
1 year ago
0
implement Consensus Hit Support
#20
taylorreiter
closed
1 year ago
1
implement HGT-finder
#19
taylorreiter
closed
1 year ago
2
implement DarkHorse algorithm to interpret BLASTp hits (lineage probability index; LPI)
#18
taylorreiter
closed
1 year ago
1
PR roadmap for release 1
#17
taylorreiter
opened
1 year ago
0
remove eggnog annotation in favor of kofamscan
#16
taylorreiter
closed
1 year ago
3
Quick PR to remove unused env files
#15
taylorreiter
closed
1 year ago
0
figure out database release plan
#14
taylorreiter
closed
1 year ago
1
Start merging nextflow repo with this repo by renaming and updating R scripts
#13
taylorreiter
closed
1 year ago
0
change RAAU filtering to be a percentage of pangenome size, not an absolute number (150 right now)
#12
taylorreiter
closed
1 year ago
1
add `distinct()` to the final combined results TSV to remove duplicated rows
#11
taylorreiter
closed
1 year ago
1
prepend HGT score values with rank (0, 1, 2, etc) so they can be sorted in a heirarchically meaningful way
#10
taylorreiter
closed
1 year ago
1
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