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rule.smk
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rule.smk
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# Define sample names which will be used to make panel of normals.
PON_SAMPLES = ['sample1', 'sample2']
rule create_read_count_panel_of_normals:
input:
# Required inputs in either hdf5 or tsv format.
# Inputs should be generated by running CollectReadCounts.
count_files = expand('result/{sample}/{sample}.counts.hdf5', sample=PON_SAMPLES)
# Optional inputs. Omit if unused.
# GC-content annotated-intervals file from AnnotateIntervals.
# If specified, explicit GC-bias correction will be performed on the panel samples,
# and identically for subsequent case samples.
annotated_intervals = ''
output:
# Required output PON file. MUST be hdf5 format.
'pon.hdf5'
params:
# Optional parameters. Omit if unused.
extra = '',
threads: 1
log: 'logs/gatk/create-read-count-panel-of-normals/PON.log'
wrapper:
'http://dohlee-bio.info:9193/gatk/cnv/create-read-count-panel-of-normals'