SCExecute Command and Filename Template Substutition
SCExecute can replace a variety of placeholder terms in the specified command and/or filename templates to ensure cell-barcode specific BAM files can have a cell-barcode specific command execution, output capture, and working directory, as needed. The placeholders are specified inside curly braces { and } and are uppercase (case-sensitive), as shown below.
Generated cell-barcode specific BAM file placeholders
{}
Full path to generated cell-barcode speicific BAM file.
{CBPATH}
Full path to generated cell-barcode specific BAM file.
{CBFILE}
Filename part of generated cell-barcode specific BAM file.
{CBBASE}
Filename part of generated cell-barcode specific BAM file, without the .bam extension.
Original input BAM file placeholders
{BAMPATH}
Full path of original input BAM file.
{BAMFILE}
Filename part of original input BAM file.
{BAMBASE}
Filename part of original input BAM file, without the .bam extension.
Miscellaneous
{BARCODE}
The cell-barcode for a cell-barcode specific BAM file.
{BFINDEX}
Index of original input BAM file.
{CBINDEX}
Index of cell-barcode from its original input BAM file.
{WORKER}
Processor index for a command execution.
Examples
Filename template
{BAMBASE}.{BARCODE}.bam
Logfile template
{BAMBASE}.{BARCODE}.log
Command template
gatk HaplotypeCaller -R human.fasta -I {} -O out/{BFINDEX}.{CBINDEX}.vcf