Docker container not fully compatible with Nextflow

Hi there,

I’m currently working on our pipeline ampliseq that includes QIIME2 for certain steps in a nextflow automated script. For this, I attempted to use directly the Docker Image for v2020.11 from, however, I recieved the error message Command 'ps' required by nextflow to collect task metrics cannot be found. Nextflow requires ps to be installed for metrics/trace/report generation in addition to a few other tools.

So I wanted to ask if you see the possibility to include ps in your docker container so that it can be used with nextflow (had only a problem with missing ps, but all others seem available, i.e. awk, date, grep, egrep, sed, tail, tee).


Hi @DaS, we would be happy to include that! Are you up for submitting a pull request to make this change? The Dockerfile in question is here: vm-playbooks/Dockerfile at master · qiime2/vm-playbooks · GitHub

@andrewsanchez is actually just getting ready to build the 2021.2 docker image, so if you get this in in the next day or two we should be able to include it in this current release.


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Hi @thermokarst, thats great! I opened a pull request.


Thanks so much, @DaS. The PR has been merged, this should be in the 2021.2 docker image, which we expect to release this week.


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