Problem with picard CollectHsMetrics - bpipe expecting an output file that was not defined as such #295
Description
I have a very strange problem with the output of picard CollectHsMetrics. bpipe throws an error and the pipeline fails although the output from CollectHsMetrics is as intended. This is my command stage:
HsMetrics = {
output.dir="intermediate_files"
exec """
$PICARD CollectHsMetrics
-I $input.bam
-O $output.bam.prefix
-R $REF
-BAIT_INTERVALS "/data/beds/Probes_merged_ok_combined_ULM_Twist_CLL_2025_1_TE-93654436_hg19.interval_list"
-TARGET_INTERVALS "/data/beds/Target_bases_covered_by_probes_combined_ULM_Twist_CLL_2025_1_TE-93654436_hg19.interval_list"
-PER_TARGET_COVERAGE ${output.bam.prefix}_per_target_coverage.bed"""
}
It takes a whatever.bam file as input and produces two statistics files: whatever.HsMetrics (the main output) and whatever.HsMetrics_per_target_coverage.bed (the optional output defined by the -PER_TARGET_COVERAGE option). I do get the files that I expect, however bpipe throws the error
"ERROR: Expected output file intermediate_files/whatever.HsMetrics.bam in stage HsMetrics could not be found"
and the pipeline fails. Why does it expect to produce a third output file ending in .bam which I have not defined in the command? The problem is not in the optional output, I tried without it and I continue getting the same error. These are the log files: [
](url)
I also tried simply with -I $input -O $output. It still works although the result file is then named whatever.bam.HsMetrics. Not that this is a problem in itself but bpipe still throws an error, this time looking for the output whatever.bam.HsMetrics.bam. Why does bpipe expect a bam file as output when CollectHsMetrics should produce only statistics?
I have never experienced anything similar with other commands including with other commands from the picard package.