text: user10415: I’m trying to create a pipeline for genome assembly. How best can I “redirect/pipe” from existing fasta files (or files in general) to other steps of the pipeline?
  I was thinking of going from the SRA Download step (prefetch and fasterq-dump) to fastqc, then to trimmomatic or bbduk to remove the adapters, one more fastqc check and then to SPAdes for the assembly.
  In my (amateur) mind it would be cool to be like:
  “SRRXXXXXX” | prefetch | fasterq-dump | fastqc | bbduk.sh | fastqc (second) | spades.py
  Any and all help is greatly appreciate! I know this stuff is pretty basic but I am so new to everything it’s painfully obvious to even me.
  
  user3252: Maybe take a look at workflow management systems, like
  
  snakemake
  Nextflow
  Toil
  Cromwell
  
  Admitted, each of those adds their additional learning curve. However, especially snakemake is not so much more complicated than a standard bash workflow. Those systems do help a lot organize and orchestrate your workflows
  
original_text: 10415: <p>I’m trying to create a pipeline for genome assembly. How best can I “redirect/pipe” from existing fasta files (or files in general) to other steps of the pipeline?</p>
  <p>I was thinking of going from the SRA Download step (prefetch and fasterq-dump) to fastqc, then to trimmomatic or bbduk to remove the adapters, one more fastqc check and then to SPAdes for the assembly.</p>
  <p>In my (amateur) mind it would be cool to be like:</p>
  <p>“SRRXXXXXX” | prefetch | fasterq-dump | fastqc | bbduk.sh | fastqc (second) | spades.py</p>
  <p>Any and all help is greatly appreciate! I know this stuff is pretty basic but I am so new to everything it’s painfully obvious to even me.</p>
   3252: <p>Maybe take a look at workflow management systems, like</p>
  <ul>
  <li><a href="https://snakemake.readthedocs.io/en/stable/index.html" rel="nofollow noreferrer">snakemake</a></li>
  <li><a href="https://nextflow.io/example1.html" rel="nofollow noreferrer">Nextflow</a></li>
  <li><a href="https://toil.readthedocs.io/en/latest/" rel="nofollow noreferrer">Toil</a></li>
  <li><a href="https://cromwell.readthedocs.io/en/stable/" rel="nofollow noreferrer">Cromwell</a></li>
  </ul>
  <p>Admitted, each of those adds their additional learning curve. However, especially snakemake is not so much more complicated than a standard bash workflow. Those systems do help a lot organize and orchestrate your workflows</p>
  