nf-core/taxprofiler

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

Stars: 194
Forks: 69
Open beginner issues: 0
Indexed issues: 47
Avg merge: 3d 6h
Merged PRs (30d): 2

Dominant language: Nextflow
License: MIT
Last GitHub push: Jul 24, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: help wanted

Beginner friendly Everything

Open All

47 open issues indexed

KrakenUniq: Passing args to taxprofiler Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/taxprofiler#772 · Opened Sep 19, 2026
Add number of reads in analysis ready fastq's Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 64/100

nf-core/taxprofiler#770 · 1 reaction · Opened Sep 14, 2026
New Profiler: Protal Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/taxprofiler#765 · Opened Aug 10, 2026
Add PanTax Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 52/100

nf-core/taxprofiler#745 · Opened May 27, 2026
MetaPhlAn requires huge amounts of RAM when running with long reads Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/taxprofiler#744 · 1 comment · Opened May 14, 2026
Add an option for BAM input Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 64/100

nf-core/taxprofiler#743 · 1 comment · Opened May 13, 2026
Database file column `db_name` allows repeated entries bvut should not Open

bug

nf-core/taxprofiler#742 · 3 comments · 1 assignee · Opened May 6, 2026
Minor nf-core/tools post-merge tasks Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 64/100

nf-core/taxprofiler#740 · Opened Apr 28, 2026
Missing taxids in centrifuge.results.txt Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/taxprofiler#722 · Opened Apr 7, 2026
Fastp content in test_falcobbduk.nf.test.snap is empty Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

nf-core/taxprofiler#717 · Opened Apr 3, 2026
New classifier: GuaCAMOLE Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/taxprofiler#680 · 1 comment · Opened Jan 27, 2026
Kraken2: add option for "--use-daemon" with the k2 wrapper Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/taxprofiler#673 · 1 comment · Opened Nov 27, 2025
Request for a KrakenUniq + Bracken + Krona workflow Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/taxprofiler#669 · 1 comment · Opened Nov 21, 2025
Feature: Option to output ready TSE -object Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

nf-core/taxprofiler#663 · 1 comment · 1 reaction · Opened Nov 11, 2025
Bowtie2 "find" process fails to read symlinks when mounted in CIFS Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 65/100

nf-core/taxprofiler#652 · 17 comments · Opened Sep 23, 2025
Providing a combined report for estimated counts table for Metaphlan Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/taxprofiler#638 · 6 comments · 1 reaction · Opened Aug 26, 2025
New profiler: singleM Open

nf-core/taxprofiler#626 · 1 assignee · Opened Jul 18, 2025
Provide custom script for merging MetaPhlAn tables for better sample name handling Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/taxprofiler#574 · 4 comments · Opened Jan 30, 2025
Add option for BBTools Clumpify optical deduplication Open

enhancement question

Difficulty 5/5 Over a week Newbie friendliness 30/100

nf-core/taxprofiler#547 · 2 comments · Opened Oct 22, 2024
Create a samplesheet for mag Open

enhancement

nf-core/taxprofiler#542 · 1 assignee · Opened Oct 10, 2024
Create samplesheets for differentialabundance Open

enhancement

nf-core/taxprofiler#541 · 1 assignee · Opened Oct 10, 2024
Add the interactive visualisation tool GRIMER Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/taxprofiler#516 · 1 comment · 1 reaction · Opened Aug 19, 2024
Have checks that if sub-parameter activate but main parameter not, error or give warning Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/taxprofiler#513 · Opened Aug 8, 2024
Add CAT/BAT/RAT for long reads Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/taxprofiler#504 · 1 comment · Opened Jun 24, 2024
Add a long read classifier: lemur Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 30/100

nf-core/taxprofiler#503 · Opened Jun 24, 2024
Merged tables not produced if not run with --run_profile_standardisation Open

documentation enhancement

Difficulty 1/5 1-3 hours Newbie friendliness 35/100

nf-core/taxprofiler#494 · 1 comment · Opened Jun 11, 2024
Add support Metabuli. Open

enhancement

nf-core/taxprofiler#492 · 1 comment · 3 reactions · 1 assignee · Opened May 31, 2024
Generate samplesheet for nf-core/mag Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/taxprofiler#449 · 4 comments · Opened Feb 15, 2024
Add Eukdetect Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/taxprofiler#361 · Opened Sep 4, 2023
Profiling: consider cross-database merge for KMCP Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/taxprofiler#353 · Opened Aug 18, 2023
Ideas: more post-processing functionality Open

enhancement question

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/taxprofiler#335 · 2 comments · Opened Jul 24, 2023
Add support for MMSeqs2 Open

enhancement

nf-core/taxprofiler#323 · 1 assignee · Opened Jul 13, 2023
Consider switching host removal to graph based reference Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/taxprofiler#297 · 10 comments · 1 reaction · Opened May 22, 2023
Taxpasta only accepts a single taxonomy although multiple could be present in database samplesheet Open

bug enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/taxprofiler#293 · 3 comments · Opened May 11, 2023
Implement kaiju-mergeOutputs Open

enhancement help wanted question

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/taxprofiler#288 · 5 comments · 1 reaction · Opened Apr 26, 2023
Provide functionality to create nf-core/mag samplesheet from final reads Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/taxprofiler#284 · Opened Apr 20, 2023
Split up MultiQC run reports between long and short reads Open

enhancement

nf-core/taxprofiler#218 · 1 assignee · Opened Jan 23, 2023
Optimisation of the resource settings Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/taxprofiler#154 · Opened Oct 25, 2022
Consider default parameters for profilers Open

question

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/taxprofiler#151 · 14 comments · 2 reactions · Opened Oct 21, 2022
Extend the profiling workflow by aligning matched reads to profiled genomes Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/taxprofiler#149 · 5 comments · 1 reaction · Opened Oct 19, 2022
Classifier: metaxa2 Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/taxprofiler#139 · 10 comments · Opened Oct 10, 2022
Classifer: CLARK-S Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/taxprofiler#122 · 2 comments · Opened Sep 5, 2022
Classifier for Nanopore reads: MEGAN-LR workflow Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/taxprofiler#119 · 2 comments · Opened Sep 5, 2022
Add sourmash as a profiler (or similar) Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/taxprofiler#112 · 9 comments · 2 reactions · Opened Aug 29, 2022
Feature: Allow Recentrifuge as replacement for Krona Open

enhancement feature-request

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/taxprofiler#88 · 1 reaction · Opened Jun 9, 2022
Benchmarking / Comparisons Open

question

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/taxprofiler#64 · 12 comments · Opened Apr 22, 2022
Improve logging formatting via a custom Groovy class Open

enhancement low-priority

Difficulty 3/5 1-2 days Newbie friendliness 25/100

nf-core/taxprofiler#62 · Opened Apr 20, 2022

nf-core/taxprofiler

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