remove trimmomatic log - Githubissues

assemblerflow / flowcraft

FlowCraft: a component-based pipeline composer for omics analysis using Nextflow. :whale::package:

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remove trimmomatic log #192

Open cimendes opened 5 years ago

cimendes commented 5 years ago

Due to the very high IO necessary for trimmomatic's log production, some machines will halt this process to a crawl. A fix has been done in PR #178 but I don't consider this an ideal solution as it does not address the IO issue. A potential solution is to no save the log file but instead obtain the trimming statistics from the trimmed reads themselves, as it's implemmented in INNUca

jacarrico commented 5 years ago

I don't think this is an issue due to the run time of trimmomatic and it was only reported for docker on mac. The fix basically redirected the trimmomatic's log to /tmp and the only problem that can derive from there is using shifter and /tmp not being mapped. As such I don't think you should wait any time solving this. In my opinion , and as I already explained to @miguelpmachado, this is a closed subject for it would be a waste of resources to solve this.