These are chat archives for nextflow-io/nextflow

16th
Oct 2018
Paolo Di Tommaso
@pditommaso
Oct 16 2018 07:26
@bwlang mode: 'copy' should do that
ccasar
@ccasar
Oct 16 2018 08:27
Hi, I'm interested in running Nextflow with Singularity containers. Singularity provides the option to use the same container for multiple applications (http://singularity.lbl.gov/docs-recipes#apps) by running a container with singularity run --app foo roar.simg. As I understand nextflow always runs a container with singurlatiy run roar.simg. Would the engineOptions configurations work in this case?
Paolo Di Tommaso
@pditommaso
Oct 16 2018 08:29
containerOptions should do the trick
ccasar
@ccasar
Oct 16 2018 08:35
Oh, of course, thanks. Didn't look into the process directives...
Paolo Di Tommaso
@pditommaso
Oct 16 2018 08:35
:+1:
Toni Hermoso Pulido
@toniher
Oct 16 2018 09:05
@pditommaso thanks! It worked!
Paolo Di Tommaso
@pditommaso
Oct 16 2018 09:05
:ok_hand:
Luca Cozzuto
@lucacozzuto
Oct 16 2018 10:21
dear @pditommaso is there a way to resume an older run of nextflow (i.e. not the previous one)?
Paolo Di Tommaso
@pditommaso
Oct 16 2018 10:23
dear @lucacozzuto nextflow log give you the list of runs with a big hash
copy&paste that has number on the resume cli ie.
nextflow run -resume 78fa6-fa68-fa68f8a-c80ce80ec .. etc
Luca Cozzuto
@lucacozzuto
Oct 16 2018 10:24
can you also use the RUN name?
I love "golden_hypatia" :)
Paolo Di Tommaso
@pditommaso
Oct 16 2018 10:26
mee too!
Luca Cozzuto
@lucacozzuto
Oct 16 2018 10:39
however it doesn't get it
Paolo Di Tommaso
@pditommaso
Oct 16 2018 10:39
I was sure :joy:
Luca Cozzuto
@lucacozzuto
Oct 16 2018 10:39
and of course has to be my fault
:)
Paolo Di Tommaso
@pditommaso
Oct 16 2018 10:39
obviously !
Luca Cozzuto
@lucacozzuto
Oct 16 2018 10:40
yes
eheheheh
btw is this documented somewhere
is super nice feature
Paolo Di Tommaso
@pditommaso
Oct 16 2018 10:41
no
Caspar
@caspargross
Oct 16 2018 12:39

hey! i try to execute an awk command containing $ signs in my script and found the advice from paolo to work with shell: (https://github.com/nextflow-io/nextflow/issues/157#issuecomment-219706124 )
However i still get error messages. What am I missing?

shell:
 """
readLength=$(zcat !{sr1} | awk "NR % 4 == 2 {s += length($1); t++} END {print s/t}")
echo $readLength
 """

results in the following error messag:
ERROR ~ illegal string body character after dollar sign; solution: either escape a literal dollar sign "\$5" or bracket the value expression "${5}"
I tried to escape but then the awk command stops working

Paolo Di Tommaso
@pditommaso
Oct 16 2018 12:41
you need to use single triple quote chars, not double
Caspar
@caspargross
Oct 16 2018 12:42
🤦
thaks
Paolo Di Tommaso
@pditommaso
Oct 16 2018 12:42
:+1:
Eric Davis
@davisem
Oct 16 2018 18:28
Can't lock file: nextflow/history -- Nextflow needs to run in a file system that supports file locks
I see what causes this error, so I guess my question is: is there a way around it? Can I specify the path for this file?
on LSF, if you submit a batch of nextflow commands, this error is usually thrown
I agree it
's strange to be attempting this, but I have a really good reason :)
Brad Langhorst
@bwlang
Oct 16 2018 19:02

@pditommaso : hmm, i tried this:

publishDir "${outputDir}", mode: 'copy', pattern: ‘bams_for_import’

with

mkdir bams_for_import && pushd bams_for_import && ln -s ../!{library}.md.bam .

in the script
That did not copy anything to the output directory… Did I miss your point?