These are chat archives for nextflow-io/nextflow

9th
Mar 2016
Tiffany Delhomme
@tdelhomme
Mar 09 2016 10:10

Hi Paolo, just one question, to reduce the code, could it be possible to have an input like

file bam from bams
file bais.filter{ it =~ 'bam.baseName' }

or do we have to necessarily use mapped pairs? I guess pair method is better if a bam does not have its bai mate...

for the moment I get the error not such variable: bam
Paolo Di Tommaso
@pditommaso
Mar 09 2016 10:12
no, that's not possible
wait
not sure I've understood well what you are trying to do
Tiffany Delhomme
@tdelhomme
Mar 09 2016 12:47
Actually I have one folder containing bam files and associated bai files.
I would like to run a tool on each bam-bai pair which need a bam in input and its bai (not in input but present in the executing folder).
It works if I use phase() and map() to group the pairs, but I asked myself if there is a way without paired the bam-bai but by taking in input bai corresponding to the bam (the form is ID.bam ID.bam.bai)...
Paolo Di Tommaso
@pditommaso
Mar 09 2016 12:47
oh sorry I was interrupted
the point is that nextflow symlink the input files in the task work directory
so you need to provide all the files that are need properly
you can simplify it using a map followed by groupTuple
like in this exmaple
Tiffany Delhomme
@tdelhomme
Mar 09 2016 13:01
yes it is why I just wanted to symlink the bai corresponding to the 'nextflow-selected' bam with filter()...
ok I will look at this!
Lukas Jelonek
@lukasjelonek
Mar 09 2016 15:22
Hey, I have a question regarding the s3 support. Is it possible to use s3 compatible providers or is it restricted to amazon?
Paolo Di Tommaso
@pditommaso
Mar 09 2016 15:28
@lukasjelonek as long as the provider it is compatible with the S3 API it should work
Lukas Jelonek
@lukasjelonek
Mar 09 2016 15:54
Do I have to use full URLs then? Or can I configure the something?
Paolo Di Tommaso
@pditommaso
Mar 09 2016 16:08
@lukasjelonek yes, you should configure some provider dependant API end-points, but I'm really sure that is possibile to define them
Lukas Jelonek
@lukasjelonek
Mar 09 2016 16:08
Thanks, I will just try it and come back if it fails :)
Paolo Di Tommaso
@pditommaso
Mar 09 2016 16:09
well, will fail surely because it will try to connect to the AWS storage
let me check the config options
so, AWS S3 endpoint can be specified on the URL like the following
s3://s3-us-west-2.amazonaws.com/bucket_name/some/path/..
In theory you should be able to replace s3-us-west-2.amazonaws.com with the endpoint of your provider, but I'm not sure that it will work
if it fails please open an issue on github specifying your provider details
Lukas Jelonek
@lukasjelonek
Mar 09 2016 16:14
Okay, I'll give it a try