# Which module do you want to run?
# select between Gaia, Rhea, Perses, Pallas and DepthFilter
runScript: DepthFilter
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#---------------------------------DepthFilter-------------------------------------#
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atlas: conda
sampleFile: fromGaia
ref: ../Reference/hs37d5.fa
parallelize: T
binCount: 10
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# optional parameters
# atlasParams: general atlas parameters applying to all jobs unless specified within the job parameters. default: ""
# Attention: do not use option "--chr" if "parallelize" is used (which is the default)! use config parameter "chromPar:" instead.
# pileupParams: specific parameters to pass for Atlas-task pileup
# Attention: do not use option "--chr" if "parallelize" is used (which is the default)! use config parameter "chromPar:" instead.
# pileupToBedParams: specific parameters to pass for Atlas-task pileupToBed
#
# parallelize: run pileup tasks in parallel for each chromosome group. Output bed filter files will then be concatenated into one outfile. default=T
# binCount: if parallelize=T you can additionally set a number of bins for parallelization. default=10
# chromPar: if you want to restrict your parallelization on a certain set of chromosomes, add them here as a comma separated string. example: "scaffold_1,scaffold_3,scaffold4". If "F", default=all (all contigs in BAM header considered)
#
#
# depthFilterOut: save DepthFilter bed file with a different prefix. this can be useful to produce outfiles with different filter options
# quantile: choose quantile of depth for depth filter cutoff. Default=0.99
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# general parameters
# atlas: specify if Atlas should automatically be loaded from conda whenever necessary (default: conda). If you would like to use a pre-compiled Atlas instead, set argument to the path for the executable.
# tmpDir: specify a temporary directory to be used. default: [$TMPDIR]
#
# outPath: specify the name of the results folder.
# In case you refer to prior modules (with fromGaia, fromRhea, etc.)
# these results must be in the same folder as well. default: results
#