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

• DEPRECATED- New parameter mmseqs_cluster_mode default to 0 (#130)
• Refactor module arguments to pipeline arguments (#166)

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