TLDR
Enter a command. For example: gh pr create, sc im, img2pdf.

nextflow

 
Tool for running computational pipelines. Mostly used for bioinformatics workflows. More information: https://www.nextflow.io.
 
  • Run a pipeline, use cached results from previous runs:
     
    nextflow run {{main.nf}} -resume
     
  • Run a specific release of a remote workflow from GitHub:
     
    nextflow run {{user/repo}} -revision {{release_tag}}
     
  • Run with a given work directory for intermediate files, save execution report:
     
    nextflow run {{workflow}} -work-dir {{path/to/directory}} -with-report {{report.html}}
     
  • Show details of previous runs in current directory:
     
    nextflow log
     
  • Remove cache and intermediate files for a specific run:
     
    nextflow clean -force {{run_name}}
     
  • List all downloaded projects:
     
    nextflow list
     
  • Pull the latest version of a remote workflow from Bitbucket:
     
    nextflow pull {{user/repo}} -hub bitbucket
     
  • Update Nextflow:
     
    nextflow self-update

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