Ian Light-Maka
Ian Light-Maka
no longer implementing, functionality in latest release of kraken2
will still implement, since functionality is _slightly_ different
the complexity filtering should be close to done now, oepend a PR. subworkflow for metagenomics screening tools is going to be started tomorrow when @ilight1542 and @merszym are in person...
now working on this on branch metagenomics-pairedend current status: input into krakenuniq working using both a mixture of PE and SE job submissions, that then are all kept in the...
Current status for naming conventions allowed: Checked in eager/subworkflows/local/utils_nfcore_eager_pipeline/main.nf - No mixed strandedness for the same sample across different libraries is allowed. (eg all data for sampleA must be single...
should consider also implementing this enhancement for bam filtering https://github.com/nf-core/eager/issues/945
RE: keeping strandedness. Since the only meta in malt-run is the meta with the list of read files, keeping info on which samples have single-stranded library prep must be done...
@jfy133 -- I think it is all set for review once more: a quick update RE: strandedness going into metagenomics screening. The current way that bamfiltering is done, the per-sample...
Note: when adding multivcf analyzer ploidy MUST be set at 2 for unified genotyper. Current default behavior is that any fasta without explicit ploidy will be set at ploidy 2...
Pull #1126 is basically 2 main sets of changes - (1) I think should definitely be maintained, (2) I do not have strong opinions on (and the adjustment/functionality is relatively...