1.2.5
Version of tools in docker image (/container/Dockerfile)
Tool
Version
Location
ubuntu
16.04
-
GetBaseCountMultiSample
1.2.5
https://github.com/msk-access/GetBaseCountMultiSample/releases/tag/1.2.5
CWL
CWL specification 1.0
Use example_inputs.yaml to see the inputs to the cwl
Example Command using toil:
> toil-cwl-runner getbasecountmultisample_1.2.5.cwl example_inputs.yaml
If at MSK, using the JUNO cluster having installed toil-msk version 3.21.1 you can use the following command
#Using CWLTOOL
> cwltool --singularity --non-strict /path/to/getbasecountmultisample_1.2.5.cwl /path/to/inputs.yaml
#Using toil-cwl-runner
> toil-cwl-runner --singularity --logFile /path/to/gbcms_toil.log --jobStore /path/to/gbcms_jobStore --batchSystem lsf --workDir /path/to/gbcms_toil_log --outdir . --writeLogs /path/to/gbcms_toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --disableChaining --maxLogFileSize 20000000000 /path/to/getbasecountmultisample_1.2.5.cwl /path/to/inputs.yaml > gbcms_toil.stdout 2> gbcms_toil.stderr &
Usage
usage: getbasecountsmultisample_1.2.5.cwl [-h]
[--memory_per_job MEMORY_PER_JOB]
[--memory_overhead MEMORY_OVERHEAD]
[--number_of_threads NUMBER_OF_THREADS]
--genotyping_bams GENOTYPING_BAMS
--genotyping_bams_ids
GENOTYPING_BAMS_IDS
--filter_duplicate FILTER_DUPLICATE
--fragment_count FRAGMENT_COUNT
--maf MAF [--maq MAQ] [--omaf]
--output OUTPUT --ref_fasta
REF_FASTA [--vcf VCF]
[--generic_counting GENERIC_COUNTING]
[job_order]
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
--genotyping_bams GENOTYPING_BAMS
Input bam file
--genotyping_bams_ids GENOTYPING_BAMS_IDS
Input bam, sample identifier to be used for "Tumor
Sample Barcode" for maf or Sample name in the header
for vcf
--filter_duplicate FILTER_DUPLICATE
Whether to filter reads that are marked as duplicate.
0=off, 1=on. Default 1
--fragment_count FRAGMENT_COUNT
Whether to output fragment read counts DPF/RDF/ADF.
0=off, 1=on. Default 0
--maf MAF Input variant file in TCGA maf format. --maf or --vcf
need to be specified at least once. But --maf and
--vcf are mutually exclusive
--maq MAQ Mapping quality threshold. Default 20
--omaf Output the result in maf format
--output OUTPUT Filename for output of raw fillout data in MAF/VCF
format
--ref_fasta REF_FASTA
Input reference sequence file
--vcf VCF Input variant file in vcf-like format(the first 5
columns are used). --maf or --vcf need to be specified
at least once. But --maf and --vcf are mutually
exclusive
--generic_counting GENERIC_COUNTING
se the newly implemented generic counting algorithm.
Works better for complex variants. You may get
different allele count result from the default
counting algorithm
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