I personally like keeping the BAM files for the final long and short read coverage calculations, because users can then check how reads mapped in specific places to look for abnormalities. However, from a high-throughput perspective, the BAM files waste a lot of space. What would you think about adding a setting in the config (e.g., keep_bam_files) that users can turn on so that the final BAM files are not treated as temp()? We could leave the setting False by default. This config setting could be used in a rule like this:
mapping="{sample}/annotation/coverage/{sample}_short_read.bam" if keep_bam_files else temp("{sample}/annotation/coverage/{sample}_short_read.bam")
This would apply to calculate_final_short_read_coverage and calculate_final_long_read_coverage.
jmtsuji
commented
5 months ago
I personally like keeping the BAM files for the final long and short read coverage calculations, because users can then check how reads mapped in specific places to look for abnormalities. However, from a high-throughput perspective, the BAM files waste a lot of space. What would you think about adding a setting in the config (e.g.,
keep_bam_files) that users can turn on so that the final BAM files are not treated astemp()? We could leave the setting False by default. This config setting could be used in a rule like this:This would apply to
calculate_final_short_read_coverageandcalculate_final_long_read_coverage._Originally posted by @jmtsuji in https://github.com/rotary-genomics/rotary/pull/114#discussion_r1482665387_