These are chat archives for nextflow-io/nextflow

5th
Dec 2017
Luca Cozzuto
@lucacozzuto
Dec 05 2017 15:21
Hi Paolo, before a make an issue do you have a way to clean the work dir removing the subfolder that are not needed for a re-run?
(imagine I re-run several times the pipeline changing params and I want to keep the latest run but removing the other attempts)
Paolo Di Tommaso
@pditommaso
Dec 05 2017 15:22
check the nextflow clean command
Luca Cozzuto
@lucacozzuto
Dec 05 2017 15:25
there is no help?
Paolo Di Tommaso
@pditommaso
Dec 05 2017 15:26
yes ..
$ nextflow clean -h
Clean up project cache and work directories
Usage: clean [options] 
  Options:
    -after
       Clean up runs executed after the specified one
    -before
       Clean up runs executed before the specified one
    -but
       Clean up all runs except the specified one
    -n, -dry-run
       Print names of file to be removed without deleting them
       Default: false
    -f, -force
       Force clean command
       Default: false
    -h, -help
       Print the command usage
       Default: false
    -q, -quiet
       Do not print names of files removed
       Default: false
:satisfied:
Luca Cozzuto
@lucacozzuto
Dec 05 2017 15:27
ok so now that I have an execution running I can use -before (what??)
should I add a pid?
Félix C. Morency
@fmorency
Dec 05 2017 15:28
run name
-before crazy_coconut
Luca Cozzuto
@lucacozzuto
Dec 05 2017 15:30
mmm (lets'add it to the help!!)
Paolo Di Tommaso
@pditommaso
Dec 05 2017 15:30
if you offer me a coffee I will tell you :satisfied:
Luca Cozzuto
@lucacozzuto
Dec 05 2017 15:30
Neither -f or -n specified -- refused to clean
if you come now there is also a cake
Paolo Di Tommaso
@pditommaso
Dec 05 2017 15:31
deal !
Luca Cozzuto
@lucacozzuto
Dec 05 2017 15:33
ERROR ~ Unable to acquire lock on session with ID b92d847d-91e9-4a66-b40b-dfc58263bc7f

Common reasons of this error are:
 - You are trying to resume the execution of an already running pipeline
 - A previous execution was abruptly interrupted leaving the session open

You can check what process is holding the lock file by using the following command:
 - lsof /nfs/users/bi/sequencing_analysis/ekizito/2017-11-10-Solanum_SNPs/analysis/.nextflow/cache/b92d847d-91e9-4a66-b40b-dfc58263bc7f/db/LOCK
Félix C. Morency
@fmorency
Dec 05 2017 15:34
I don't think you can clean while an execution is running
Luca Cozzuto
@lucacozzuto
Dec 05 2017 15:34
yes I noticed
Félix C. Morency
@fmorency
Dec 05 2017 15:34
I believe this could lead to caching issues
Luca Cozzuto
@lucacozzuto
Dec 05 2017 15:35
it will be nice to have it somewhere and also to refuse the cleaning if there is an instance running
I hope not