Giters
NBISweden
/
aMeta
Ancient microbiome snakemake workflow
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Stargazers:
20
Watchers:
9
Issues:
80
Forks:
14
NBISweden/aMeta Issues
errors after cutadapt
Updated
2 months ago
Remote providers have been replaced
Updated
3 months ago
Comments count
17
Failed to extract ref_id from results/AUTHENTICATION/
Updated
3 months ago
Comments count
8
Breadth of coverage needs to depend on MaltExtract output being generated
Updated
3 months ago
Comments count
2
MapDamage is not generating expected output
Updated
3 months ago
Comments count
3
krakendb/taxDB and krakendb/taxDB.
Updated
3 months ago
Comments count
1
issue with krakenuniq output when running on KrakenUniq full NCBI NT database
Closed
3 months ago
Comments count
8
Test not working
Closed
3 months ago
Comments count
8
Error in rule Plot_Authentication_Score when using FULL NCBI database
Closed
a year ago
Comments count
20
different versions of FastQC give different adapter stats
Updated
4 months ago
OSError: [Errno 39] Directory not empty: 'envs'
Updated
5 months ago
Missing Assigned Taxon IDs
Updated
5 months ago
Comments count
2
Some reference genomes are assigned to several taxIDs which generate noise at the mapDamage part
Closed
5 months ago
Comments count
1
Python syntax of Malt-build script doesn't work with Python 3.12.1
Closed
5 months ago
Comments count
11
The png file for authentication plots doesn't render well on mac
Closed
5 months ago
Comments count
2
add --large-index to the Bowtie2_Index rule
Closed
5 months ago
Comments count
7
Error in Authentication_Score
Closed
5 months ago
Comments count
6
Bug in Authentication_Score rule
Closed
5 months ago
Comments count
2
Default parameters in MaltExtract leading missing output
Closed
5 months ago
Comments count
3
Add rulegraph to README.
Closed
5 months ago
Comments count
2
add scientific names to taxIDs in results/AUTHENTICATION and malt_abundance_matrix_rma6.txt
Updated
5 months ago
mem_mb in FastQC rule should be changed
Closed
5 months ago
Comments count
3
get_ref_id sometimes doesn't take the best reference genome for the organism depending on the structure of the MaltExtract output
Updated
6 months ago
Comments count
1
Updating FastQC rules
Closed
10 months ago
change -j4 for testrun
Closed
10 months ago
Change default frontend for installations depending on conda>=23.10.0
Closed
10 months ago
add possibility for "sequence" rank when filtering KU output
Updated
a year ago
How to run only krakenuniq part of the pipeline? (A specific option in the config file is needed)
Updated
a year ago
Comments count
1
aMeta is loading KU DB individually for each sample
Updated
a year ago
Comments count
1
Options or instructions for users with PE sequencing data
Closed
a year ago
Comments count
1
skip adapter removal step
Closed
a year ago
Comments count
3
Deamination takes too much time for large samples
Closed
a year ago
Comments count
1
Java heap space error on MaltExtract
Closed
a year ago
Comments count
1
Need to add -threads: 1 to all rules as a default
Closed
a year ago
Comments count
1
Authentication plots pdf files are too heavy
Closed
a year ago
Comments count
1
Add pysam to the workflow/envs/mapdamage.yaml
Closed
a year ago
Comments count
3
MaltExtract has trouble finding ncbi.map and ncbi.tre files
Closed
a year ago
Comments count
1
problem with MapDamage
Closed
a year ago
Comments count
5
The authentication plots are generated with different malt outputs and the amount of reads therefore don't correspond.
Updated
a year ago
Comments count
1
No validator found for JSON Schema version identifier
Closed
a year ago
Comments count
4
Usage of default MALT parameters
Closed
a year ago
Comments count
1
A rule is using pathogen specific file for filtering which should not be the case.
Closed
2 years ago
Comments count
1
MapDamage is only applied to pathogens
Closed
2 years ago
Comments count
1
Error: duplicates in sam-header when running Bowtie2 on full NT
Closed
2 years ago
Comments count
2
Option to choose between filtering by TaxReads or Reads
Closed
2 years ago
Comments count
2
RScript fails with one sample
Closed
2 years ago
Comments count
1
mapdamage rule fails when no pathogen present
Closed
2 years ago
Comments count
1
no full pathogen list pathogensFound.very_inclusive.tab is provided in aMeta repo
Closed
2 years ago
Comments count
3
Malt_quantify_abundance rule broken
Closed
2 years ago
Comments count
1
filter_krakenuniq, krakenuniq2krona, krakenuniq_abundance_matrix scripts overlap
Closed
2 years ago
Comments count
2
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