Change check_own process to not include input files in output #113
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hoelzer
approved these changes
Nov 12, 2024
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Resolves #107
Only when you are using a self-provided reference file, you would get duplicates in your reference file at some point. This was caused by the
check_ownprocess, which did this:seqkit seq {input} -o {output}.gzand then returns any gzip files including those in the input. This causes a problem when the input file has a .gz extension, leading to both the input and seqkit output files being passed on to the next process, which combines both files together and renames any duplicates.Resolved by disabling "includeInputs" and also I used a fixed output file name and explicitly passed that on. Feel free to tweak this change if you like but it should resolve the problem.