distiller 0.3.5 roadmap

[agalitsyna]

I included here only the issues that are either easy small fixes or structural changes that are important and also easy to introduce.

• [ ] Support minimap2, bwa aln, bwa mem2 https://github.com/open2c/distiller-nf/issues/181
• [ ] Add short read alignment for reads <25 bp https://github.com/open2c/distiller-nf/issues/141
• [ ] Add adaptor trimming https://github.com/open2c/distiller-nf/issues/146
• [ ] Fix sra-toolkit issue: https://github.com/open2c/distiller-nf/issues/157
• [ ] Fix exhausted suffixes: https://github.com/open2c/distiller-nf/issues/169
• [ ] Option to start from bam files: https://github.com/open2c/distiller-nf/issues/178

[Phlya]

We discussed adding filters to stats in distiller and @agalitsyna tried something, but in the end we never implemented it... Shall we do it? I propose to add the --filter 'name"expression' arguments to the dedup command, and also --yaml to actually store all the filter outputs?