> toil-cwl-runner manta_1.5.1.cwl example_inputs.yaml
#Using CWLTOOL
> cwltool --singularity --non-strict /path/to/manta_1.5.1/manta_1.51.cwl /path/to/inputs.yaml
#Using toil-cwl-runner
> mkdir toil_log
> toil-cwl-runner --singularity --logFile /path/to/toil_log/cwltoil.log --jobStore /path/to/jobStore --batchSystem lsf --workDir /path/to =toil_log --outdir . --writeLogs /path/to/toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 /path/to/manta_1.5.1/manta.1.5.1.cwl /path/to/inputs.yaml > toil.stdout 2> toil.stderr &
> toil-cwl-runner manta_1.5.1.cwl --help
usage: manta_1.5.1.cwl [-h]
positional arguments:
job_order Job input json file
optional arguments:
-h, --help show this help message and exit
--memory_per_job MEMORY_PER_JOB
Memory per job in megabytes
--memory_overhead MEMORY_OVERHEAD
Memory overhead per job in megabytes
--number_of_threads NUMBER_OF_THREADS
--call_regions CALL_REGIONS
bgzip-compressed, tabix-indexed BED file specifiying
regions to which variant analysis will be restricted
--non_wgs toggles on settings for WES
--normal_bam NORMAL_BAM
Normal sample BAM or CRAM file. May be specified more
than once, multiple inputs will be treated as each BAM
file representing a different sample. [optional] (no
default)
--output_contigs if true, outputs assembled contig sequences in final
VCF files, in the INFO field CONTIG
--reference_fasta REFERENCE_FASTA
samtools-indexed reference fasta file [required]
--tumor_bam TUMOR_BAM
Tumor sample BAM or CRAM file. Only up to one tumor
bam file accepted.
--generateEvidenceBam
Generate a bam of supporting reads for all SVs
