Nextflow basic pipeline

[crosenth]

1. Create one container with all dependencies

Pipeline:

1. cmalign query sequences to 16s profile
2. esl-alimerge query and reference alignments
3. pplacer
4. guppy classifications classifications.db
5. Reports (get_classifications.py, sv_table.R, label_taxon_table.py)

@nhoffman

[crosenth]

1. Get rid of (bio)scons from requirements.txt
2. Convert biopython requirement to fastalite, see bin/downsample(.py)
3. R Phyloseq package needs to be found from somewhere (in dada2-nf image currently) Just use the dada2-nf image for now

[crosenth]

1. Drop cmfilter.py step because dada2-nf is already doing (may want to put this back in later)
2. Use dada-nf Docker image (package) for entire pipeline

[crosenth]

Additional pipeline dependencies from dada2-nf:

1. pplacer and guppy
2. taxtastic and sqlalchemy
3. FastTree (Phyloseq rds file)

[crosenth]

Use taxtastic image for pplacer, guppy and do not create Phyloseq object