bhattlab bhattlab_workflows issues

bhattlab / bhattlab_workflows

Computational workflows for metagenomics tasks, by the Bhatt lab

http://www.bhattlab.com

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issues

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containers: documentation and scripts for building the preprocessing container.

#47 cosnicolaou closed 1 year ago
0
das_tool version needs to be added in the YAML file

#46 Anqi-Dai closed 2 years ago
1
metariboseq updates

#45 cosnicolaou closed 2 years ago
0
fastANI not installed in the drep docker image

#44 Anqi-Dai closed 3 years ago
1
rgi error with multiple contigs of same name

#43 bsiranosian opened 3 years ago
0
binning workflow optimizations

#42 tamburinif closed 3 years ago
1
add metariboseq to top level README

#41 cosnicolaou closed 3 years ago
0
minor updates to metariboseq README.

#40 cosnicolaou closed 3 years ago
0
mge-hotspots: add support for annotation and finding closest genes and intergenic hotspots.

#39 cosnicolaou closed 3 years ago
0
mge-hotspots: workflow for finding mobile insertion 'hotspots'

#38 cosnicolaou closed 3 years ago
0
use github (ghcr.io) as the docker container registry

#37 cosnicolaou closed 3 years ago
0
metariboseq/containers: the docker files for building metariboseq docker containers

#36 cosnicolaou closed 3 years ago
0
metariboseq: initial checkin for the metariboseq pipeline

#35 cosnicolaou closed 3 years ago
0
updating assembly

#34 skong822 closed 4 years ago
1
Updated SRA snakefile using fasterq-dump

#33 navajain closed 4 years ago
0
Not sure if I did this correctly...

#32 navajain closed 4 years ago
1
Compare_bins_references concat_top_nucmer error

#31 dgmaghini closed 3 years ago
1
Add fi to if statement

#30 sevance closed 4 years ago
1
Missing fi in checkpoint metabat

#29 sevance closed 4 years ago
1
Sourmash plotting fails to create container?

#28 alvinh315 closed 4 years ago
0
Binning error when bin.tooShort is empty

#27 alvinh315 closed 4 years ago
1
Error in gplots library call in sourmash

#26 alvinh315 closed 4 years ago
1
possibility of merging of compatible bins?

#25 dgmaghini opened 5 years ago
0
Spades often gets stuck on read error correction

#24 bsiranosian opened 5 years ago
0
Merge Sort reads branch with master

#23 bsiranosian closed 5 years ago
0
Demultiplexing tip for undetermined fastq files

#22 bfremin opened 5 years ago
3
Preprocessing breaks on sample names that are only numbers

#21 bfremin closed 4 years ago
2
Preprocessing_TrimGalore eroor

#20 chrissev closed 5 years ago
3
syncing script is not flexible with header formats

#19 tamburinif closed 5 years ago
3
Containerized preprocessing

#18 elimoss closed 5 years ago
1
rule post_fastqc fails if there are no orphans

#17 elimoss closed 5 years ago
1
shouldn't preprocessing use EXTENSION?

#16 elimoss closed 5 years ago
1
cleanup rule works but throws some errors -- clean up

#15 tamburinif closed 4 years ago
0
scripts dir??

#14 tamburinif closed 5 years ago
1
Compatibility with single-end data

#13 tamburinif closed 5 years ago
1
Test dataset and branching

#12 bsiranosian closed 3 years ago
2
Change dedup program?

#11 tamburinif closed 4 years ago
5
Add gzipping of 05_sync files, script to remove all temp files

#10 bsiranosian closed 5 years ago
1
add .gitignore to stop commiting of hiddenfiles

#9 bsiranosian closed 5 years ago
1
change to sync script in this repo, specify in config file

#8 bsiranosian closed 5 years ago
0
Lost sync.py script commit?

#7 tamburinif closed 5 years ago
1
One Step Closer...

#6 chrissev closed 5 years ago
0
Sync file does not keep output files in the right order

#5 jribado closed 5 years ago
0
PreProcessing Workflow in SnakeMake

#4 chrissev closed 5 years ago
1
Snakemake Workflow

#3 chrissev closed 5 years ago
3
Snakemake work-file (Syntax error in preprocessing workflow)

#2 chrissev closed 5 years ago
3
Preprocessing needs to output a table for assembly

#1 elimoss closed 6 years ago
1