nf-core/viralmetagenome
Detect iSNV and construct whole viral genomes from metagenomic samples
epidemiologyfastqngsviral-metagenomicsvirologyvirus-genomes
Version history
Second release of the viralgenie pipeline. Focusing on user experience and bug fixes.
Enhancement
- 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)
Fixed
- 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
Parameters
Initial pre-release with core functionalities.
What’s Changed
- Update versions by @Joon-Klaps in #117
- combine multiple functions of preclustering into one by @Joon-Klaps in #111
- 102 autodetect paired end by @Joon-Klaps in #109
- 65 select best ref by @Joon-Klaps in #107
- 105 out of memory during network cluster process on unclassified taxa by @Joon-Klaps in #106
- Continue making docs by @Joon-Klaps in #104
- 61 update docs make release by @Joon-Klaps in #103
- Handling singletons by @Joon-Klaps in #101
- Include bwamem mapper + multifasta support + virosaurs annotation by @Joon-Klaps in #100
- Fixing dev by @Joon-Klaps in #99
- Revert “49 samplesheet mapping constrains” by @Joon-Klaps in #97
- Add clean_output_on_error parameter and implement directory deletion … by @Joon-Klaps in #94
- Modules update by @Joon-Klaps in #92
- Annotate with mmseqs instead of blast by @Joon-Klaps in #91
- Making hybrid scaffold optional by @Joon-Klaps in #89
- Alignment free deduplication by @Joon-Klaps in #87
- template v2.12 by @Joon-Klaps in #86
- Add annotation of final contigs by @Joon-Klaps in #83
- Add “subject title” column to blast_df and update ext.args in modules… by @Joon-Klaps in #82
- 67 multiqc report for quast include assemblers by @Joon-Klaps in #81
- Joon klaps/include krona report by @Joon-Klaps in #79
- Add seqkit/replace module for string replacement in sequences by @Joon-Klaps in #77
- Add changelog configuration bot v0.1dev by @Joon-Klaps in #76
- Joon klaps/mpileup calling without reference by @Joon-Klaps in #71
- Add global prefix to publishDir paths by @Joon-Klaps in #70
- Add fastp deduplication option and accuracy parameter by @Joon-Klaps in #69
- 49 samplesheet mapping constrains by @Joon-Klaps in #60
- Update input parameters in make_bed_mask.nf, main.nf, and mem.nf by @Joon-Klaps in #59
- module version bump by @Joon-Klaps in #54
- Template update by @Joon-Klaps in #53
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last release
4 months ago
last update
4 months ago
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