These are chat archives for nextflow-io/nextflow

30th
Oct 2017
Luca Cozzuto
@lucacozzuto
Oct 30 2017 12:26
hi this does not seem a problem of nextflow. check in the working folder if the links are there and the error of the aligner
Ghost
@ghost~598345d2d73408ce4f6ff925
Oct 30 2017 14:07
I think it's an issue with the way the reads are put into the channel
basically I need to figure out how to put the gzipped reads into a channel that can be recognize with this input comman set sampleid, file (reads:'*') from gzipped_reads
Luca Cozzuto
@lucacozzuto
Oct 30 2017 14:15
gzipped or not the channel does not care about it... have you checked the working folder?
Ghost
@ghost~598345d2d73408ce4f6ff925
Oct 30 2017 15:02
I got it!
also, is there a way to force a process to execute last?
Luca Cozzuto
@lucacozzuto
Oct 30 2017 15:03
?
you mean to be executed at the end?
Ghost
@ghost~598345d2d73408ce4f6ff925
Oct 30 2017 15:09
yes
Luca Cozzuto
@lucacozzuto
Oct 30 2017 15:12
this is inherently done by nextflow. Basically by describing input and output (and process order) you implicitly tell the program what to execute first and last.
Ex: process 1 has input reads and output alignments. Process 2 has input alignments and output read counts. Process 3 collects the read counts into a single matrix (output). Process 4 use the matrix as input to make clustering (output).
Ghost
@ghost~598345d2d73408ce4f6ff925
Oct 30 2017 15:16
yes, hmmm it's tough because I have some conditionals in the config file that can turn on/off some processes so multiqc doesn't always run at the end depending on what's being skipped. Maybe I'll output a fake file from all the second to last process options and use that as an input for multiqc
Luca Cozzuto
@lucacozzuto
Oct 30 2017 15:18
or you can put multiqc under the same condition
you can have if (condition==TRUE) then process multiqc
Phil Ewels
@ewels
Oct 30 2017 21:52
We use if blocks and make fake empty channels instead of when for this reason šŸ‘šŸ»
If there is a better way Iā€™d be keen to hear it!
Paolo Di Tommaso
@pditommaso
Oct 30 2017 21:53
there's but I'm too tired to explain sorry .. :)
Mike Smoot
@mes5k
Oct 30 2017 21:54
Also interested to hear about that solution... tomorrow! :)