groovy oneliner to get first token/column of tsv file

[colindaven]

Dear all,

this is dsl 2.0

I know I can use file(somefile.fai).readLines() to read a whole file. If the file only contains one column (chromosome name) this works great.

fai_channel = Channel
    //.fromList(file(params.fai).readLines())
    //.fromList(file(prepare_fai.out).readLines())
    //.fromList((prepare_fai.out).readLines())
    .fromList(file(params.fai).readLines().splitEachLine("\t"))
    .map { [ it ] }
    .view()

But can I just read the first column of the tab separated TSV in a one liner? Eg split by tab, then get the 0th token.

I've tried using a process to prepare a multi-column TSV (fai file) into a single column one using
cut -f 1 x.fai > x.fai.txt
, but then I can't seems to read it using file(prepare_fai.out) above.

If not, would another method (eg value channel) be compatible with the .map I want to do here ?

Thanks!
Colin

[phue]

Hi Colin,

.splitText() allows to specify a closure, so something like this should to the trick:

Channel
 .fromPath(params.fai)
 .splitText( each:{ it.split().first() } )
 .view()

Cheers,
Patrick

[colindaven]

Thanks Patrick, that worked a treat. Now I guess I'll have to read up a bit more on groovy closures ...
cheers,
Colin