Giters
NBISweden
/
aMeta
Ancient microbiome snakemake workflow
Geek Repo:
Geek Repo
Github PK Tool:
Github PK Tool
Stargazers:
19
Watchers:
9
Issues:
80
Forks:
14
NBISweden/aMeta Issues
The png file for authentication plots doesn't render well on mac
Updated
9 months ago
Updating FastQC rules
Closed
10 months ago
change -j4 for testrun
Closed
10 months ago
Add rulegraph to README.
Updated
10 months ago
Comments count
1
add --large-index to the Bowtie2_Index rule
Updated
10 months ago
Comments count
6
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
10 months ago
Some reference genomes are assigned to several taxIDs which generate noise at the mapDamage part
Updated
10 months ago
How to run only krakenuniq part of the pipeline? (A specific option in the config file is needed)
Updated
10 months ago
Comments count
1
issue with krakenuniq output when running on KrakenUniq full NCBI NT database
Closed
10 months ago
Comments count
6
Error in rule Plot_Authentication_Score when using FULL NCBI database
Closed
10 months ago
Comments count
19
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
Remove trailing sam 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
Pathogen-only projects
Closed
2 years ago
Comments count
7
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
Warning regarding path for log file
Closed
2 years ago
Comments count
3
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
Some interesting microbes are ignored because they are labelled as "no rank" in the ncbi database
Updated
2 years ago
Comments count
3
no full pathogen list pathogensFound.very_inclusive.tab is provided in aMeta repo
Closed
2 years ago
Comments count
3
Rule PMD_score failing with no error message
Closed
2 years ago
Comments count
6
Malt_quantify_abundance rule broken
Closed
2 years ago
Comments count
1
add nextera adapter removal
Closed
2 years ago
filter_krakenuniq, krakenuniq2krona, krakenuniq_abundance_matrix scripts overlap
Closed
2 years ago
Comments count
2
Impossible to give more threads to the rule "KrakenUniq2Krona"
Closed
2 years ago
Comments count
1
seqtk subseq is slow on large databases
Closed
2 years ago
Comments count
1
cannot extract refid
Closed
2 years ago
Comments count
3
The Malt_QuantifyAbundance rule takes la long time to run
Closed
2 years ago
Malt_Extract fails due to missing entries in custom ncbi.map
Closed
2 years ago
Comments count
1
krakenuniq-build v.0.7.3 cannot find jellyfish
Closed
2 years ago
Comments count
2
Use rule names verbatim in messages
Closed
2 years ago
Add flag --number 100000 to the PMDtools rule
Closed
2 years ago
Erroneous combinations of taxid and refids
Closed
2 years ago
Comments count
1
Post_Processing rule fails due to missing input data?
Closed
2 years ago
Comments count
1
checkpoint rules produce different amount of outputs depending on target type
Closed
2 years ago
Comments count
1
Previous
Next