muse.template

#####
# If generating JSON for multiple samples, replace '</full/file/path>' or 'null' with '<>', then complete muse.sample_list.tab. See
# ./backup_templates/muse.sample_list.template for examples. Be certain to provide a unique identifier under the 'run_uid' header to
# clearly distinguish samples/runs. If *optional* sample-specific values are desired, the appropriate key from this template may be used as
# a column header in muse.sample_list.tab (be careful to maintain tab-delimited format).
####
tumor: {
    class: File
    path: </full/file/path>         # Required file; replace '</full/file/path>' with full path to tumor DNA BAM file [e.g., /my/path/to/tumor.bam]
normal: {
    class: File
    path: </full/file/path>         # Required file; replace '</full/file/path>' with full path to normal DNA BAM file [e.g., /my/path/to/normal.bam]
reference: {
    class: File
    path:  </full/file/path>       # Required file; replace '</full/file/path>' with full path to reference FASTA [e.g., /my/path/to/genome.fa.gz]
known: {
    class: File
    path: </full/file/path>         # Required file; replace '</full/file/path>' with full path to dbSNP VCF file [e.g., /my/path/to/dbsnp.vcf]
mode: null                          # Optional enum value; valid options are wgs or wxs; 'null' defaults to 'wxs'
ncpus: null                         # Optional integer; number of threads to run MuSE; 'null' defaults to '8'