These are chat archives for nextflow-io/nextflow

1st
Sep 2017
Ashley S Doane
@DoaneAS
Sep 01 2017 00:36
to not use singularity for a specific process, can I add something like singularity.enabled = false in the process? I seem to get an error about the singularity variable. thanks
Anthony Underwood
@aunderwo
Sep 01 2017 08:11
@pditommaso Thanks for pointing me at :

it mentions in the builder a mounts key. This is then reflected in mounts created in the YAML file
https://github.com/nextflow-io/nextflow/blob/master/src/test/groovy/nextflow/executor/KubernetesExecutorTest.groovy#L202-L208

How would these mounts be specified when running Nextflow?

Paolo Di Tommaso
@pditommaso
Sep 01 2017 12:39
@DoaneAS yes, add the following setting in the config file process.$yourTaskName.container = null
@aunderwo these mounts are automatically inferred by NF depending the process inputs, as it would do when using a docker w/o kubernetes
Anthony Underwood
@aunderwo
Sep 01 2017 15:25
I know nextflow usually creates work directory in $PWD . How do you specify somewhere else? Using the scratch directive?
Paolo Di Tommaso
@pditommaso
Sep 01 2017 16:01
with the -w command line option or NXF_WORK variable
Anthony Underwood
@aunderwo
Sep 01 2017 16:01
OK cool thanks
Paolo Di Tommaso
@pditommaso
Sep 01 2017 16:02
:+1: