The format is based on Keep a Changelog and this project adheres to Semantic Versioning.
Second release of the viralgenie pipeline. Focusing on user experience and bug fixes.
- Set default umitools dedup strategy to cluster (#126)
- Include both krakenreport &nodes.dmp in taxonomy filtering (#128)
- Add Sspace indiv to each assembler seperatly (#132)
- Add read & contig decomplexification using prinseq++ (#133)
- Add option to filter contig clusters based on cumulative read coverage (#138)
- Reffurbish mqc implementation (#139)
- Adding mash-screen output to result table (#140)
- Add logic to allow samples with no reference hits to be analysed (#141)
- Add visualisation for hybrid scaffold (#143)
- Add new module to inculde custom mpileup-vcf file for intra-host analyses (#151)
- Update docs (#150)
- Make custom-mpileup.py postion 1 index based and not 0 index to follow bcftools (#153)
- Update docs for more streamlined docs & figures (#154)
- Add column in custom mpileup - Shannon entropy (#156)
- Constrain -> Constraint & further python script debugging (#161)
- include empty samples in multiqc sample overview (#162)
- Include samtools stats pre dedup & post dedup in overview tables (#163)
- adding prokka for gene detection & annotation (#165)
- OOM with longer contigs for nocov_to_reference, uses more RAM now (#125)
- fixing null output from global prefix (#147)
- Fix empty filtered clusters (#148)
- Fixing missing columns from general stats & add general stats sample filtering (#149)
- process.shell template fix (#157) - see also nf-core/tools #3416
- New parameter mmseqs_cluster_mode default to 0 (#130) DEPRECATED
- Refactor module arguments to pipeline arguments (#166)
Initial release of Joon-Klaps/viralgenie, created with the nf-core template.