Open
Milestone
Issues en vrac
Unstarted Issues (open and unassigned)
17
- Improve HiFi binning
- test the taxonomic asffiliation improvment at the contig level by taxometer
- Investigate Sylph perhaps to replace kaiju
- improve functionnal annotation
- Improvment siggested by Maria
- binning : benschmark of other tools / methods
- provide the possibility to give the metaflye infos of circular contigs as input at the same time as the assembly
- Duplicate clustering if coassembly all samples
- Refactoring
- Add info if bin is RNA complete or not
- Minimap2 requires an extra parameter for large reference (>4GB)
- Re-activate the workflow installation with conda
- Add taxonomic affiliation plots to multiqc
- Eggnog mapper chunks
- Questions to answer with the pipeline (biologist)
- Bins and contigs: generate matrix with metrics
- Clustering: improve table_clstr.txt
Ongoing Issues (open and assigned)
13
- Replace diamond by MMseq2? (benchmark)
- replace conda by micromamba in image builder
- consistency in argument names
- use Gunc on bins to measure and visualize chimeric bins
- Add flagstat on dereplicated MAG on results files
- improve checkM2 database managing
- Make binning results compatible with anvio
- Functional test: check process and image, nextflow stub and gitlab CI/CD
- Databases saving folder
- Functional tests: change output to table format
- Documentation: update use_case.md with interpretations
- 03_filtering: Assess the impact of CPM and contig length filtering
- Metrics on final quantification file with annotations
Completed Issues (closed)
23
- La création de l'environnement conda metagWGS ne marche pas sur genotoul.
- Singularity: find a solution to have a relative env folder usage
- busco DB link initialization error (use --skip_busco)
- Fix column names for single sample
- Améliorations possibles du pipeline
- tester Apptainer
- test and propose metaMDBG assembler for pacbio HiFi reads
- use new version of gtdbtk because it correct the bug with pplacer
- test MetaMDBG
- Simplify software version scrapping
- Check the consistency between the results files
- check and correct differences in (assembly) results for functional tests
- Understanding why RGI (with prodigal) predicts more genes than metagWGS (with prokka)
- Sample names in MultiQC report
- Simplifier les paramètres de taxonomy
- Multiple singularity files (one by process)
- Usage of Markdown for use case output integration
- "split" Step 05_alignment
- Verify DIAMOND best hit strategy
- Add taxonomy db parameters
- Taxonomic affiliation of contigs and bins exploration
- nextflow.config file: manage memory and CPUs
- Transformation of prokka gff file in gtf file to take into account introns
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