These are chat archives for nextflow-io/nextflow
0.26.0-beta4with a lot of changes
[Task monitor] DEBUG nextflow.Session - Session aborted -- Cause: Missing output file(s) `blabla.pdf` expected by process `trio_excap_qc_join (1)`
.exitcodefile, after that assumes the other must be available ..
.exitcodeand my output file, and they show both the same time,
We have found that this has been an issue with our workflows requiring a 200Gb boot disk at /
docker system prune --volumes
docker system prune -adeleted images meaning that you have to keeping on pulling the images. Therefore --volumes would be required
alias docker-cleanup='X=$(docker ps -aq) && [[ $X ]] && docker rm $X; X=$(docker images -f dangling=true -q) && [[ $X ]] && docker rmi $X'
is that built in into nextflow?
docker ... --entrypoint /usr/bin/env bash ...
--entrypoint /usr/bin/env bashdoesn't work as I feared
/bin/bash. I would change it to
singularity exec xxx.img /bin/bash -c “cd $PWD; /bin/bash -ue /path/to/.command.sh”. So this means the path to workdir must be the same inside and outside the container, am I correct?
autoMounts = true