These are chat archives for nextflow-io/nextflow

3rd
Jun 2017
Shellfishgene
@Shellfishgene
Jun 03 2017 12:19
I mean for example I have 2 samples, and fastqR1/2 from one channel, and a contig file from another like above. You have to make sure the fastq from sample A does not run with the contig from sample B, no?
Maarten van Gompel
@proycon
Jun 03 2017 12:30
Is there no way I can tell nextflow to catch multiple input files with a glob pattern and just stage them with the original filename rather than rewrite it numbered? I keep running into filename preservation issues with multiple input/output files.
(to line 146), I'm batching the files in groups of 1000 to the frog_original process and want to keep the filenames, but don't really know how to do that best
Paolo Di Tommaso
@pditommaso
Jun 03 2017 15:15
@proycon use * to avoid input file rename eg
file "*" from foliadocuments_batches_tokenized1
or
Maarten van Gompel
@proycon
Jun 03 2017 15:16
ah! without any further patterns, that makes sense, thanks :)
giving it a try
Paolo Di Tommaso
@pditommaso
Jun 03 2017 15:16
file just_a_var_name from foliadocuments_batches_tokenized1
Maarten van Gompel
@proycon
Jun 03 2017 15:17
a simple var name also works then it's a collection of multiple files?
Paolo Di Tommaso
@pditommaso
Jun 03 2017 15:17
yes
Maarten van Gompel
@proycon
Jun 03 2017 15:17
great
Paolo Di Tommaso
@pditommaso
Jun 03 2017 15:17
it will hold a collection of files
ah, 0.25 includes a new file method to get the file name file.simpleName
nextflow-io/nextflow#354
Maarten van Gompel
@proycon
Jun 03 2017 15:18
oh! that sounds nice, regardless of the number of extensions? (like .tar.gz, that saves a whole lot of getBaseName() calls)
perfect
Paolo Di Tommaso
@pditommaso
Jun 03 2017 15:19
exactly
Maarten van Gompel
@proycon
Jun 03 2017 15:19
I guess the 0.25 release will be soonish?
Paolo Di Tommaso
@pditommaso
Jun 03 2017 15:20
next week hopefully
enjoy (leaving)
Maarten van Gompel
@proycon
Jun 03 2017 15:20
great, I'll just try on the snapshot for then
thanks!