nf-core/taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
NextflowMIT
Issues
- 0
No logo in multiqc report
#488 opened by jfy133 - 0
- 0
The run_accession and sample_name should be unique.
#483 opened by sofstam - 4
KrakenUniq read extraction
#474 opened by SannaAb - 1
Recommended procedure for profiling nanopore data
#480 opened by bcpd - 0
- 1
taxprofiler krona output files missing
#479 opened by aslangabriel99 - 1
Move/copy DB troubleshooting content from Usage/Tutorial to Usage/ or new Usage/Database-troubleshooting
#456 opened by vmkalbskopf - 4
Failed to produce kaiju_combined_reports.txt
#460 opened by LilyAnderssonLee - 1
Current UNTAR scheme inefficent and can cause overwriting for database sheet input
#462 opened by jfy133 - 8
Allow hibf in ganon?
#401 opened by SannaAb - 0
Profiling: consider cross-database merge for KMCP
#353 opened by jfy133 - 10
Adding GetOrganelle
#414 opened by erinyoung - 4
Generate samplesheet for nf-core/mag
#449 opened by CarsonJM - 1
Replace samplesheet check with nf-validation for both sample and database input sheets
#336 opened by jfy133 - 1
Logo does not match the logo in tube
#452 opened by sofstam - 13
- 0
- 0
kaiju2table not reporting taxon names
#431 opened by sofstam - 1
Simplify test profiles in CI test
#374 opened by LilyAnderssonLee - 0
KMCP profile mode forced for all databases
#358 opened by jfy133 - 0
Add support for MMSeqs2
#323 opened by jfy133 - 4
- 18
- 0
General version update of all tools
#403 opened by jfy133 - 4
- 0
Add Nanoq for Nanopore reads
#415 opened by sofstam - 5
`KRONA_KTIMPORTTEXT` input file name collision if same 'db_name' is assigned to kraken2 and bracken
#395 opened by MajoroMask - 1
Allow multiple bracken profiles with different `-l` levels from the same kraken2 report
#410 opened by MajoroMask - 5
- 3
- 1
Taxpasta parameters produce an error exit status of 2 which asks for a taxonomy even though kraken2 and centrifuge have worked.
#390 opened by alimalrashed - 1
MetaPhlAn4 full index provide duplicated 'NCBI_tax_id' to taxpasta as input
#396 opened by MajoroMask - 1
Taxpasta parameters produce an error exit status of 2 which asks for a taxonomy even though kraken2 and centrifuge have worked.
#391 opened by alimalrashed - 1
- 0
Update to nf-core tempate 2.10
#382 opened by jfy133 - 0
- 0
Add small files to tower.yml
#373 opened by LilyAnderssonLee - 0
Add Eukdetect
#361 opened by maxibor - 5
Decontamination: add hostile for host removal
#346 opened by jfy133 - 2
Write a short getting started tutorial
#340 opened by jfy133 - 0
- 0
- 2
Use quickBAM
#344 opened by sofstam - 0
CENTRIFUGE produces a wrong, kraken-like report by mistakenly using the report.txt file
#337 opened by LilyAnderssonLee - 2
Ideas: more post-processing functionality
#335 opened by jfy133 - 1
- 2
- 3
ERROR: Missing required column header -> sample
#328 opened by kneubehl - 2
Add functionality to turn read QC on/off
#324 opened by vinisalazar