frederic-mahe / fred-metabarcoding-pipeline-nextflow

Fred's metabarcoding pipeline with Nextflow

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fred-metabarcoding-pipeline-nextflow

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)

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Fred's metabarcoding pipeline with Nextflow

License:GNU General Public License v3.0


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