Filtered passed bedpe can be empty for ClusterSV and SVSignature input. And the original package doesn't handle this correctly, resulting the following error in a recent run.
For ClusterSV:
tail /juno/work/tempo/wgs/Francisco_20220915/workspace/work/8c/2ea5cf88081ac9198f8d2914d1d206/.command.err
The following objects are masked from ‘package:base’:
cat, commandArgs, getOption, inherits, isOpen, nullfile, parse,
warnings
Warning message:
Input file is empty.
Error in filter_by_chrom(d, chrom = rownames(centromere_telomere_coords)) :
object 'd' not found
## creating output directory if it does not exist ##
## read and pre-process input ##
Error in `$<-.data.frame`(`*tmp*`, sample, value = "OPR057B__OPR057N") :
replacement has 1 row, data has 0
Calls: $<- -> $<-.data.frame
Execution halted
We might have to handle this in our own workflow, rather than having the developer of the tools to change their code, although clearly the original code should be corrected.
Filtered passed bedpe can be empty for ClusterSV and SVSignature input. And the original package doesn't handle this correctly, resulting the following error in a recent run.
For ClusterSV:
tail /juno/work/tempo/wgs/Francisco_20220915/workspace/work/8c/2ea5cf88081ac9198f8d2914d1d206/.command.errhttps://github.com/cancerit/ClusterSV/blob/1d7eeea8f22133d811bed6a4cbbaf1ad2122e2c4/R/run_cluster_sv.R#L62-L68
For SVSignature:
We might have to handle this in our own workflow, rather than having the developer of the tools to change their code, although clearly the original code should be corrected.