ampliseq
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nf-core
Amplicon sequencing analysis workflow using DADA2 and QIIME2
### Description of feature I suggest to make it possible to run sintax instead of assignTaxonomy using all taxonomic databases currently supported by ampliseq. It should only be a matter...
### Description of feature The early steps in the pipeline run multiple samples in parallel (e.g., if there is 10 samples, fastqc gets run 10 times). This is the normal...
### Description of feature I know Ampliseq already uses fastqc, but I like using Seqkit stats when demultiplexing to track the number of reads that did and didn't get assigned...
### Description of feature I can add a module to Amliseq that would run the LCA scripts from eDNAFlow. More information can be found here: https://github.com/mahsa-mousavi/eDNAFlow#lca-lowest-common-ancestor-script-for-assigning-taxonomy The input to the...
### Description of feature Call the `fasta_newick_epang_gappa` subworkflow for _all_ ASV sequence, given user specified parameters: * `pplace_tree` (A tree in newick format) * `pplace_aln` (The corresponding alignment in fasta...
### Description of feature If `--pplace` or not `--skip_pplace` run phylogenetic placement with standard data. Add reference data to taxonomy reference configs so that: Accept a list of taxa in...
### Description of feature Would it be possible to add support for Oxford Nanopore Technology reads? I've found two projects (the second integrating the first) that might allow a quick...
Version `2.14.1` of [nf-core/tools](https://github.com/nf-core/tools) has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline. Please make sure to...
### Description of feature Hi, Thanks for developing Ampliseq! I was wondering whether a metadata file is really necessary for the visualisation of the relative microbial abundance per sample. Currently,...
### Description of the bug The error massage says: ``` The following samples had too few reads (
