These are chat archives for nextflow-io/nextflow

9th
Jan 2015
Andrew Stewart
@andrewcstewart
Jan 09 2015 00:28
Alright @pditommaso now I have a complex enough question for the google group :)
ill ask it there
Paolo Di Tommaso
@pditommaso
Jan 09 2015 13:31
@andrewcstewart Hi. There's no difference between $foobar and ${foobar} in the script block
They are two alternative syntax for variables interpolation into a string
The only difference is that the curly brackets allows you to enter an expression statement in place of a simple variable
Andrew Stewart
@andrewcstewart
Jan 09 2015 18:29
Ah
Thanks
I thought it had something to do with input types
val vs file
Andrew Stewart
@andrewcstewart
Jan 09 2015 18:43
Im creating a read_pairs channel similar to the RNAseq pipeline example on the website..
but I'm creating my reads1 and reads2 channels by performing an (reads1,reads2) = Channel.fromPath("/path/to/*fastq.gz").into(2) , followed by a filters on both channels and finally phase()ing them together
but it looks like my read pairs are mismatched
suggesting that the two read channels are not in the same order
does phase not preserve order?
Andrew Stewart
@andrewcstewart
Jan 09 2015 19:12
hmm phase might not be what I want here
Andrew Stewart
@andrewcstewart
Jan 09 2015 19:53
figured it out
man phase is a weird function
Paolo Di Tommaso
@pditommaso
Jan 09 2015 22:24
@andrewcstewart What's wrong with the phase operator ?
:)
Andrew Stewart
@andrewcstewart
Jan 09 2015 23:25
Oh nothing
probably
haha
there might be a bug...
I was trying to do a phase operator on two channels where the matching key is the 2nd element of the list that each channel emits
I thought I was writing my map function properly but I guess not
anyway I just moved the matching key to the first position in the list and it worked