/kea2

Primary LanguagePython

  • environment & directory based parameters
  • multi level templates
  1. basic cl
samtools view -Sb input.sam > output.bam
  1. annotate cl to identify components -> perfect provenance tracking
{x} samtools view -Sb {i} input.sam > {o} output.bam
  1. expand wildcards
{x} samtools view -Sb {i} {name~*}.sam > {o} {name}.bam
  1. reuseable snippets
{x} samtools view -Sb {<} {{name~*}}.sam > {>} {{name}}.bam

wildcard expansion

  • *.bam
  • {*}.bam