achillesrasquinha/16SMaRT

TODO

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achillesrasquinha commented

Description

  • #2
  • Data Logger for Data Dump
  • Error Issues
  • Check where CSV data is fetched from.
  • Check if SRA already exists.
  • Check if FASTQ already exists.
  • mothur acting poorly with grouped FASTA files. (Check)
  • configure SILVA version
  • Create Status check.
  • Build Geo Graph
  • Create Base Image for CI
  • Better Data Handling for mothur
  • TQDM + ProcessPool + Build Function
  • Add CSV URL getter.
  • Add URL for FASTQ optional.
  • Configure Preprocess.
  • Perform FastQC after fasterqdump
  • Multiple DataBases (https://github.com/tseemann/sixess)
  • Support GZ and use GZ for minimal output.
  • Support other HPC systems (https://blog.jwf.io/2019/08/hpc-workloads-containers/)
  • Create Flow Diagram
  • Default Truncation Length (min_length, max_length)
  • Support other based pipelines DADA2, QIIME. Also support 18s + ITS pipelines.

Updated

  • Issue running FASTQC
  • Parallelize Groups
  • FASTQC not accepting input

Screenshot

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