These are chat archives for nextflow-io/nextflow

15th
Dec 2016
amacbride
@amacbride
Dec 15 2016 00:14
It does! Very cool.
amacbride
@amacbride
Dec 15 2016 00:36
In answer to the comments from yesterday about storeDir and publishDir in the same process, it doesn't seem to work quite as expected. When I run the following the first time, I end up with nothing in the publishDir, and the expected output in the storeDir. The second time I run it (leaving the existing files in place), I get a NullPointerException. Will paste in the stack.
process onlyfoo {
        echo true
        cpus 8
        memory "545m"
        storeDir '/tmp/theoutput'
        publishDir '/tmp/thepublish', mode: "copy"

        output:
                file testout

    when:
                params.product == "foo"

    script:
                """
                echo "hello from script" > testout
                date >> testout
                """
}
amacbride
@amacbride
Dec 15 2016 00:42
N E X T F L O W  ~  version 0.22.6
Launching `mem.nf` [sad_elion] - revision: 43132d0d9a
[warm up] executor > slurm
[skipping] Stored process > onlyfoo (1)
ERROR ~ Error executing process > 'onlyfoo (1)'

Caused by:
  java.lang.NullPointerException


 -- Check '.nextflow.log' file for details
Error: null
Full report: Error executing process > 'onlyfoo (1)'

Caused by:
  java.lang.NullPointerException

Pipeline completed at: Wed Dec 14 16:33:38 PST 2016
Paolo Di Tommaso
@pditommaso
Dec 15 2016 10:27
@amacbride please open an issue on GH about that
amacbride
@amacbride
Dec 15 2016 22:14
will do