Fred's metabarcoding pipeline with Nextflow
This is a first attempt at converting to Nextflow the pipeline I use for my own metabarcoding projects.
Current status:
- draft of the first section of the pipeline (process individual samples),
- collect info from log files,
- add checks:
- user-set parameters (empty strings, unrealistic values?),
- dependencies and minimal versions (vsearch, cutadapt, swarm, bash >= 4),
- adapt to work with slurm,
- automatically deduced the fastq file naming pattern,
- automatically deduced compression (gz, bz2) or the lack-of,
- extend to multiplexed datasets,
- draft of the second section of the pipeline (work at the study scale)