• environment & directory based parameters
• multi level templates

1. basic cl

samtools view -Sb input.sam > output.bam

2. annotate cl to identify components -> perfect provenance tracking

{x} samtools view -Sb {i} input.sam > {o} output.bam

3. expand wildcards

{x} samtools view -Sb {i} {name~*}.sam > {o} {name}.bam

4. reuseable snippets

{x} samtools view -Sb {<} {{name~*}}.sam > {>} {{name}}.bam

wildcard expansion

• *.bam
• {*}.bam