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vdblab
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vdblab-shotgun
Shotgun metagenomic sequencing processing pipeline
MIT License
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Compress kraken2.out files?
#94
miraep8
opened
1 month ago
0
Clean up the temporary annotation outputs
#93
miraep8
opened
1 month ago
0
Trimming: parameter tuning?
#92
miraep8
opened
1 month ago
3
Feature/qc step ds kraken
#91
nickp60
closed
2 months ago
5
Release/0.4.13
#90
nickp60
closed
2 months ago
0
Host read removal: use human pangenome reference
#89
funnell
opened
5 months ago
0
WIP trimming resources
#88
nickp60
closed
5 months ago
1
Can we parse the kmer output of fastqc to estimate de-duplication memory requirements?
#87
nickp60
opened
5 months ago
0
Parallelize some of our bash scripts better
#86
miraep8
opened
6 months ago
0
add test data generation workflow
#85
nickp60
closed
6 months ago
0
Updating the Cazyme Annotation Pipeline
#84
miraep8
closed
5 months ago
0
Feature/mgx single end
#83
nickp60
closed
6 months ago
1
Concatenate host reference genomes for depletion steps rather than running sequentially
#82
nickp60
opened
6 months ago
0
Hotfix to annotate part 3
#81
miraep8
closed
7 months ago
0
Merging Nick's annotation update
#80
miraep8
closed
7 months ago
0
Adding hotfix from main branch
#79
miraep8
closed
7 months ago
0
extended the run time for slow rule in annotate
#78
miraep8
closed
7 months ago
11
Annotation (`annotate_annotate_CAZI_split`) Timeouts
#77
miraep8
closed
7 months ago
0
Change submodule validates
#76
miraep8
closed
8 months ago
4
SortMeRNA Timeouts
#75
nickp60
closed
6 months ago
5
Updating the README.md with environment hints for new users.
#74
miraep8
closed
10 months ago
8
remove shards from assembly for easier importing
#73
nickp60
opened
10 months ago
0
add minimizer output to kraken
#72
nickp60
opened
12 months ago
0
Split kraken rule to not run kraken and phanta
#71
nickp60
opened
1 year ago
0
Add entropy filter to bbduk
#70
nickp60
opened
1 year ago
1
Release/0.4.2
#69
nickp60
closed
1 year ago
0
update super-linter
#68
funnell
closed
1 year ago
0
Adding Phanta integrated prophage detection
#67
funnell
closed
1 year ago
3
test.sh issues
#66
funnell
closed
1 year ago
2
annotation.smk complaining about missing assembly file even when assembly stage not running
#65
funnell
closed
1 year ago
2
`SNAKEMAKE_PROFILE` env var undefined when --profile set
#64
funnell
closed
1 year ago
2
bowtie_human jobs killed due to hitting memory limit
#63
funnell
opened
1 year ago
5
PSA: Use Snakemake >= 7.19
#62
nickp60
closed
1 year ago
1
incorporate phanta into kraken stage
#61
nickp60
closed
1 year ago
0
Fix/predetermine annotation assembly chunks
#60
nickp60
closed
1 year ago
1
tune annotation metaerg resources
#59
nickp60
closed
1 year ago
0
join_CAZI ProtectedOutputException error
#58
nickp60
closed
1 year ago
1
Fix/host read parallel
#57
nickp60
closed
1 year ago
0
Release/0.4.0
#56
nickp60
closed
1 year ago
0
bump biobakery for parallel indexing
#55
nickp60
closed
1 year ago
0
Feature/megahit
#54
nickp60
closed
1 year ago
0
Assemblies Stalling
#53
nickp60
closed
1 year ago
1
Feature/multilib spades
#52
nickp60
closed
1 year ago
1
Fix/downsample multiple fastqs
#51
nickp60
closed
1 year ago
0
temp uncompressed unclassified fastqs, and fix cases with exact read lengths for bracken
#50
nickp60
closed
1 year ago
0
Bam merge files exist
#49
nickp60
closed
1 year ago
0
ModuleNotFoundError: No module named 'pandas' Error in rule preprocess_merge_logs_for_multiqc:
#48
funnell
closed
1 year ago
3
Feature/skip sample2markers
#47
nickp60
closed
1 year ago
5
Create .snakemake-workflow-catalog.yaml
#46
nickp60
closed
1 year ago
1
bump biobakery with fix to minpath
#45
nickp60
closed
1 year ago
1
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