NBISweden aMeta issues - Githubissues

NBISweden / aMeta

Ancient microbiome snakemake workflow

MIT License

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issues

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Enhancement: Create a folder AUTHENTICATION_PLOTS_PDF and output the pdf plots there and AUTHENTICATION_PLOTS_PNG and output the png plots there

#178 ZoePochon opened 5 days ago
0
--preload-size instead of --preload for KrakenUniq

#177 ZoePochon opened 1 week ago
0
Defaults should be removed from the conda environments

#176 mahesh-panchal opened 2 weeks ago
0
Missing Input Files Error at 'prepare and run aMeta' Stage

#175 libby-natola opened 3 weeks ago
3
errors after cutadapt

#174 Sevgi-k opened 3 months ago
1
Add nox test setup

#173 percyfal opened 4 months ago
0
Add conda version check to update conda frontend in test

#172 percyfal closed 5 months ago
1
Failed to extract ref_id from results/AUTHENTICATION/

#171 mudymudy opened 5 months ago
8
Breadth of coverage needs to depend on MaltExtract output being generated

#170 ZoePochon opened 5 months ago
2
krakendb/taxDB and krakendb/taxDB.

#169 CJJ8848 opened 5 months ago
1
Remote providers have been replaced

#168 LeandroRitter opened 5 months ago
17
different versions of FastQC give different adapter stats

#167 LeandroRitter opened 5 months ago
0
Test not working

#166 mudymudy closed 5 months ago
8
MapDamage is not generating expected output

#165 rozwalak opened 6 months ago
4
OSError: [Errno 39] Directory not empty: 'envs'

#164 LeandroRitter opened 6 months ago
0
add scientific names to taxIDs in results/AUTHENTICATION and malt_abundance_matrix_rma6.txt

#163 LeandroRitter opened 6 months ago
0
fixing multiple issues

#162 LeandroRitter closed 6 months ago
0
Bug in Authentication_Score rule

#161 LeandroRitter closed 6 months ago
2
Use custom github action for snakemake v7

#160 percyfal closed 6 months ago
0
changes typo in qc.smk

#159 FreyaStein closed 6 months 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 7 months ago
1
Error in Authentication_Score

#157 renatolatorre closed 6 months ago
6
mem_mb in FastQC rule should be changed

#156 LeandroRitter closed 6 months ago
3
Python syntax of Malt-build script doesn't work with Python 3.12.1

#155 ZoePochon closed 6 months ago
11
Missing Assigned Taxon IDs

#154 ardasevkar opened 10 months ago
2
Default parameters in MaltExtract leading missing output

#153 ardasevkar closed 6 months ago
3
Fix report links

#152 percyfal opened 10 months ago
0
The png file for authentication plots doesn't render well on mac

#151 ZoePochon closed 6 months ago
2
Add rulegraph to README.

#150 percyfal closed 6 months ago
2
Add option to turn off bowtie analyses

#149 percyfal opened 12 months ago
0
Update runtest.sh to use conda solver by default

#148 percyfal closed 12 months ago
0
Change default frontend for installations depending on conda>=23.10.0

#147 percyfal closed 12 months ago
0
Suggest -j 1 and lint readme.

#146 percyfal closed 12 months ago
1
Add memory option to fastqc and bump version dependency to 0.12.1

#145 percyfal closed 12 months ago
0
add possibility for "sequence" rank when filtering KU output

#144 LeandroRitter opened 1 year ago
0
change -j4 for testrun

#143 LeandroRitter closed 12 months ago
0
add --large-index to the Bowtie2_Index rule

#142 LeandroRitter closed 6 months ago
7
Some reference genomes are assigned to several taxIDs which generate noise at the mapDamage part

#141 ZoePochon closed 6 months ago
1
How to run only krakenuniq part of the pipeline? (A specific option in the config file is needed)

#140 emrahkirdok opened 1 year ago
1
Updating FastQC rules

#139 Thijessen closed 12 months ago
0
aMeta is loading KU DB individually for each sample

#138 julienfumey opened 1 year ago
1
Error in rule Plot_Authentication_Score when using FULL NCBI database

#137 npsonis opened 1 year ago
20
issue with krakenuniq output when running on KrakenUniq full NCBI NT database

#136 CjeicaM closed 4 months ago
8
fixed bug in score.R and added info to FAQ

#135 LeandroRitter closed 1 year ago
1
added ANI filter, vignettes, pathogens to list, fixed a few bugs, tuned fontsize for heatmaps

#134 LeandroRitter closed 1 year ago
2
MaltExtract has trouble finding ncbi.map and ncbi.tre files

#133 Thijessen closed 1 year ago
1
Add pysam to the workflow/envs/mapdamage.yaml

#132 ZoePochon closed 1 year 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