extract
Version of tools in docker image (/container/Dockerfile)
Tool
Version
Location
biometrics_extract
0.2.15
CWL
CWL specification 1.0
Use example_inputs.json to see the inputs to the cwl
Example Command using toil:
> toil-cwl-runner biometrics_extract.cwl example_inputs.json
#Using CWLTOOL
> cwltool --singularity --non-strict /path/to/biometrics_extract.cwl /path/to/example_inputs.json
#Using toil-cwl-runner
> mkdir tool_toil_log
> toil-cwl-runner --singularity --logFile /path/to/tool_toil_log/cwltoil.log --jobStore /path/to/tool_jobStore --batchSystem lsf --workDir /path/to/tool_toil_log --outdir . --writeLogs /path/to/tool_toil_log --logLevel DEBUG --stats --retryCount 2 --disableCaching --maxLogFileSize 20000000000 /path/to/biometrics_extract.cwl /path/to/example_inputs.json > tool_toil.stdout 2> tool_toil.stderr &
Usage
> toil-cwl-runner biometrics_extract.cwl -h
usage: biometrics_extract/0.2.15/biometrics_extract.cwl [-h] --sample_bam SAMPLE_BAM
[--sample_sex SAMPLE_SEX]
[--sample_group SAMPLE_GROUP] --sample_name
SAMPLE_NAME --fafile FAFILE --vcf_file VCF_FILE
[--bed_file BED_FILE] [--database DATABASE]
[--min_mapping_quality MIN_MAPPING_QUALITY]
[--min_base_quality MIN_BASE_QUALITY]
[--min_coverage MIN_COVERAGE]
[--min_homozygous_thresh MIN_HOMOZYGOUS_THRESH]
[--default_genotype DEFAULT_GENOTYPE]
[--file_type FILE_TYPE]
[job_order]
positional arguments:
job_order Job input json file
optional arguments:
-h, --help show this help message and exit
--sample_bam SAMPLE_BAM
BAM file.
--sample_sex SAMPLE_SEX
Expected sample sex (i.e. M or F).
--sample_group SAMPLE_GROUP
The sample group (e.g. the sample patient ID).
--sample_name SAMPLE_NAME
Sample name. If not specified, sample name is automatically figured out from the
BAM file.
--fafile FAFILE Path to reference fasta.
--vcf_file VCF_FILE VCF file containing the SNPs to be queried.
--bed_file BED_FILE BED file containing the intervals to be queried.
--database DATABASE Directory to store the intermediate files after running the extraction step.
--min_mapping_quality MIN_MAPPING_QUALITY
Minimum mapping quality of reads to be used for pileup.
--min_base_quality MIN_BASE_QUALITY
Minimum base quality of reads to be used for pileup.
--min_coverage MIN_COVERAGE
Minimum coverage to count a site.
--min_homozygous_thresh MIN_HOMOZYGOUS_THRESH
Minimum threshold to define homozygous.
--default_genotype DEFAULT_GENOTYPE
Default genotype if coverage is too low (options are Het or Hom).
--file_type FILE_TYPE
Specify the type of bam file you are generating the pickle for to be incorporated
in pickle file name (Myeloid_1_L001_duplex.pickle)
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