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