tools_cnvkit_batch.cwl

Documentation for cnvkit_batch.cwl

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etal/cnvkit:0.9.5

Name	Description	Type
tumor_bam		File
bait_intervals		File?
reference		[{'type': 'record', 'name': 'cnn_file', 'fields': {'cnn_file': {'type': 'File', 'inputBinding': {'position': 2, 'prefix': '--reference'}, 'doc': 'Previously generated reference.cnn file'}}}, {'type': 'record', 'name': 'fasta_file', 'fields': {'fasta_file': {'type': ['string', 'File'], 'inputBinding': {'position': 2, 'prefix': '--fasta'}}, 'normal_bam': {'type': 'File?', 'inputBinding': {'position': 1}, 'doc': "Normal samples (.bam) used to construct the pooled, paired, or flat reference. If this option is used but no filenames are given, a 'flat' reference will be built. Otherwise, all filenames following this option will be used."}}}]
access	Regions of accessible sequence on chromosomes (.bed), as output by the 'access' command	File?
method	Sequencing protocol used for input data	['null', {'type': 'enum', 'symbols': ['hybrid', 'amplicon', 'wgs']}]
diagram	Create an ideogram of copy ratios on chromosomes as a PDF	boolean?
scatter_plot	Create a whole-genome copy ratio profile as a PDF scatter plot	boolean?
drop_low_coverage	Drop very-low-coverage bins before segmentation to avoid false-positive deletions in poor-quality tumor samples	boolean?
male_reference	Use or assume a male reference (i.e. female samples will have +1 log-CNR of chrX; otherwise male samples would have -1 chrX)	boolean?
target_average_size	Average size of split target bins (results are approximate)	int?