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NBISweden
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aMeta
Ancient microbiome snakemake workflow
MIT License
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Add nox test setup
#173
percyfal
opened
5 days ago
0
Add conda version check to update conda frontend in test
#172
percyfal
closed
1 week ago
1
Failed to extract ref_id from results/AUTHENTICATION/
#171
mudymudy
opened
1 week ago
2
Breadth of coverage needs to depend on MaltExtract output being generated
#170
ZoePochon
opened
2 weeks ago
0
krakendb/taxDB and krakendb/taxDB.
#169
CJJ8848
opened
2 weeks ago
0
Remote providers have been replaced
#168
LeandroRitter
opened
3 weeks ago
15
different versions of FastQC give different adapter stats
#167
LeandroRitter
opened
1 month ago
0
Test not working
#166
mudymudy
closed
1 week ago
8
MapDamage is not generating expected output
#165
rozwalak
opened
1 month ago
2
OSError: [Errno 39] Directory not empty: 'envs'
#164
LeandroRitter
opened
1 month ago
0
add scientific names to taxIDs in results/AUTHENTICATION and malt_abundance_matrix_rma6.txt
#163
LeandroRitter
opened
1 month ago
0
fixing multiple issues
#162
LeandroRitter
closed
1 month ago
0
Bug in Authentication_Score rule
#161
LeandroRitter
closed
1 month ago
2
Use custom github action for snakemake v7
#160
percyfal
closed
1 month ago
0
changes typo in qc.smk
#159
FreyaStein
closed
1 month ago
1
get_ref_id sometimes doesn't take the best reference genome for the organism depending on the structure of the MaltExtract output
#158
ZoePochon
opened
3 months ago
1
Error in Authentication_Score
#157
renatolatorre
closed
1 month ago
6
mem_mb in FastQC rule should be changed
#156
LeandroRitter
closed
1 month ago
3
Python syntax of Malt-build script doesn't work with Python 3.12.1
#155
ZoePochon
closed
1 month ago
11
Missing Assigned Taxon IDs
#154
ardasevkar
opened
5 months ago
2
Default parameters in MaltExtract leading missing output
#153
ardasevkar
closed
1 month ago
3
Fix report links
#152
percyfal
opened
6 months ago
0
The png file for authentication plots doesn't render well on mac
#151
ZoePochon
closed
1 month ago
2
Add rulegraph to README.
#150
percyfal
closed
1 month ago
2
Add option to turn off bowtie analyses
#149
percyfal
opened
7 months ago
0
Update runtest.sh to use conda solver by default
#148
percyfal
closed
7 months ago
0
Change default frontend for installations depending on conda>=23.10.0
#147
percyfal
closed
7 months ago
0
Suggest -j 1 and lint readme.
#146
percyfal
closed
7 months ago
1
Add memory option to fastqc and bump version dependency to 0.12.1
#145
percyfal
closed
7 months ago
0
add possibility for "sequence" rank when filtering KU output
#144
LeandroRitter
opened
7 months ago
0
change -j4 for testrun
#143
LeandroRitter
closed
7 months ago
0
add --large-index to the Bowtie2_Index rule
#142
LeandroRitter
closed
1 month ago
7
Some reference genomes are assigned to several taxIDs which generate noise at the mapDamage part
#141
ZoePochon
closed
1 month ago
1
How to run only krakenuniq part of the pipeline? (A specific option in the config file is needed)
#140
emrahkirdok
opened
7 months ago
1
Updating FastQC rules
#139
Thijessen
closed
7 months ago
0
aMeta is loading KU DB individually for each sample
#138
julienfumey
opened
8 months ago
1
Error in rule Plot_Authentication_Score when using FULL NCBI database
#137
npsonis
opened
9 months ago
20
issue with krakenuniq output when running on KrakenUniq full NCBI NT database
#136
CjeicaM
opened
9 months ago
7
fixed bug in score.R and added info to FAQ
#135
LeandroRitter
closed
9 months ago
1
added ANI filter, vignettes, pathogens to list, fixed a few bugs, tuned fontsize for heatmaps
#134
LeandroRitter
closed
11 months ago
2
MaltExtract has trouble finding ncbi.map and ncbi.tre files
#133
Thijessen
closed
9 months ago
1
Add pysam to the workflow/envs/mapdamage.yaml
#132
ZoePochon
closed
9 months ago
3
problem with MapDamage
#131
MinLuke
closed
1 year ago
5
Added info to README and changed malt-run flags to better match it with HOPS
#130
LeandroRitter
closed
1 year ago
1
Usage of default MALT parameters
#129
Thijessen
closed
1 year ago
1
Need to add -threads: 1 to all rules as a default
#128
ZoePochon
closed
9 months ago
1
Authentication plots pdf files are too heavy
#127
ZoePochon
closed
9 months ago
1
The authentication plots are generated with different malt outputs and the amount of reads therefore don't correspond.
#126
ZoePochon
opened
1 year ago
1
No validator found for JSON Schema version identifier
#125
rozwalak
closed
1 year ago
4
Java heap space error on MaltExtract
#124
Thijessen
closed
9 months ago
1
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