nf-core / taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

https://nf-co.re/taxprofiler

nf-core/taxprofiler Issues

Add CAT/BAT/RAT for long reads
Updated a month ago
Add a long read classifier: lemur
Updated a month ago
Update nonpareil to allow gzip input
Updated a month ago
Add support for the sylph profiler
Updated a month ago
Add Nanoq for Nanopore reads
Updated a month ago
Merged tables not produced if not run with --run_profile_standardisation
Updated a month ago1
KMCP profile mode forced for all databases
Closed a month ago1
Add support Metabuli.
Updated 2 months ago
KrakenUniq read extraction
Closed 2 months ago4
Add example in documentation for multiple runs of the same sample
Closed 2 months ago
The run_accession and sample_name should be unique.
Closed 2 months ago
No logo in multiqc report
Closed 2 months ago1
Recommended procedure for profiling nanopore data
Closed 3 months ago1
Database parameter validation for bracken doesn't work currently
Closed 3 months ago
taxprofiler krona output files missing
Closed 3 months ago1
Move/copy DB troubleshooting content from Usage/Tutorial to Usage/ or new Usage/Database-troubleshooting
Closed 3 months ago1
Failed to produce kaiju_combined_reports.txt
Closed 3 months ago4
Current UNTAR scheme inefficent and can cause overwriting for database sheet input
Closed 4 months ago1
Allow hibf in ganon?
Updated 4 months ago8
Profiling: consider cross-database merge for KMCP
Updated 4 months ago
Adding GetOrganelle
Closed 4 months ago10
Generate samplesheet for nf-core/mag
Updated 4 months ago4
Replace samplesheet check with nf-validation for both sample and database input sheets
Closed 5 months ago1
Logo does not match the logo in tube
Closed 5 months ago1
Centrifuge error : (ERR): mkfifo(/tmp/72.inpipe1) failed.
Closed 5 months ago13
Empty files were also published from the module samtools/fastq
Closed 6 months ago
kaiju2table not reporting taxon names
Closed 6 months ago
Simplify test profiles in CI test
Updated 7 months ago1
Add support for sequencing coverage esimates with nonpareil
Closed 8 months ago4
Krakenuniq save_reads does not give the fastq files when using PE data
Closed 8 months ago18
General version update of all tools
Updated 8 months ago
Documentation: Broken Links in "Full database sheet" Section
Closed 8 months ago4
`KRONA_KTIMPORTTEXT` input file name collision if same 'db_name' is assigned to kraken2 and bracken
Closed 9 months ago5
Allow multiple bracken profiles with different `-l` levels from the same kraken2 report
Updated 9 months ago1
megan version 6.21.7 throw `java.lang.NullPointerException` error
Closed 9 months ago5
process `VISUALIZATION_KRONA` mis-combined channel by wrong index
Closed 9 months ago3
Taxpasta parameters produce an error exit status of 2 which asks for a taxonomy even though kraken2 and centrifuge have worked.
Closed 9 months ago1
MetaPhlAn4 full index provide duplicated 'NCBI_tax_id' to taxpasta as input
Closed 10 months ago1
Taxpasta parameters produce an error exit status of 2 which asks for a taxonomy even though kraken2 and centrifuge have worked.
Closed 10 months ago1
process `MEGAN_RMA2INFO` JavaFX detected no fonts error
Closed 10 months ago1
Update to nf-core tempate 2.10
Closed 10 months ago
Update KrakenUniq to 1.0.4 due to bug causing misreading if input files
Closed 10 months ago
Add small files to tower.yml
Updated 10 months ago
Add Eukdetect
Updated a year ago
Decontamination: add hostile for host removal
Updated a year ago5
Write a short getting started tutorial
Closed a year ago2
Enhance Profiler ganon by adding combineProfilesWithDatabase
Closed a year ago
https://github.com/nf-core/taxprofiler/pull/318
Closed a year ago
Use quickBAM
Closed a year ago2
CENTRIFUGE produces a wrong, kraken-like report by mistakenly using the report.txt file
Closed a year ago