Add --RNA option to vdb_shotgun workflow

[nickp60]

Things that would need to be changed

• change spade's --meta to --rna

[SSRAJ017]

1. Will also need to remove retroviral RNA sequences.
2. Does rRNA get removed by SortMeRNA or do we need to add a separate step for this?
3. Can consider standalone SAMSA2 addition. https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2189-z

[nickp60]

For the sortmerrna removal option we need to :

• add something like a deplete_16S option to runconfig.yaml

• add rule to be run post trimming with bbmap to use the blast ioutput from sortmeran and the trimmed fastqs to output fastqs without rrna.

  1. pull out the first column from the blast results (`zcat path/to/blast.results | cut -f 1 > 16s_reads )
  2. use inversed seqkit grep to pull out the non-16s reads from the fastqs ( seqkit grep tmpall/trimmed/473_shard001_trim_R1.fastq.gz -f tmp_16Ss --invert-match > reads1.fastq, same for reads2)

• make a function in common.smk similar to files_to_trim (https://github.com/vdblab/vdblab-pipelines/blob/2d7096e46b0595340e23cb016419cb8d77b88250/vdb_shotgun/rules/common.smk#L41) that will be used to set the inputs for the host depletion rules (replacing the trimmed files).

[nickp60]

I found this helpful https://carpentries-incubator.github.io/snakemake-novice-bioinformatics/09-input_functions/index.html

[SSRAJ017]

For RNA runs, change metaphlan directory in taxonomic-profile to metaphlan directory from paired DNA shotgun run, additional config option.