These are chat archives for nextflow-io/nextflow

1st
Oct 2018
marchoeppner
@marchoeppner
Oct 01 2018 05:38
good morning! I need some help with this: https://groups.google.com/forum/#!topic/nextflow/sZkqAbzmwPY
output statement is: set val(indivID), val(sampleID), val(libraryID), val(rgID), val(platform_unit), val(platform), val(platform_model), val(center), val(run_date),file("_R1.trimmed.fastq.gz"),file("_R2.trimmed.fastq.gz") into outputTrimAndSplit
and the transpose statement: inputBwa = outputTrimAndSplit.transpose( by: [0,1,2,3,4,5,6,7,8] )
throws: ERROR ~ Not a valid transpose element at index: 0 -- Offending tuple:
I am probably misunderstanding something about transpose ;)
Paolo Di Tommaso
@pditommaso
Oct 01 2018 06:16
please use triple ` to make code/errors more readable
then yes, not sure you need such a by with so many indexes
marchoeppner
@marchoeppner
Oct 01 2018 06:26
I think my mistake was to think that this behaves like "groupBy" - which it doesn't. Using the index of the two embedded lists (left mate, right mate) works fine
and sorry, will use proper quoting next time ^^
Paolo Di Tommaso
@pditommaso
Oct 01 2018 06:29
if you get rid of by it should work as you are expecting
process foo {

  output:
  set val('sample_x'), val('patient_y'), file('*_R1.trimmed.fastq.gz'), file('*_R2.trimmed.fastq.gz') into foo_ch

  script:
  '''
    touch 001.reads_R1.trimmed.fastq.gz 001.reads_R2.trimmed.fastq.gz
    touch 002.reads_R1.trimmed.fastq.gz 002.reads_R2.trimmed.fastq.gz
    touch 003.reads_R1.trimmed.fastq.gz 003.reads_R2.trimmed.fastq.gz
  '''
}

foo_ch
    .transpose()
    .println()
[sample_x, patient_y, /Users/pditommaso/projects/demo/work/15/fea3e3ffbad40c235865305693fda0/001.reads_R1.trimmed.fastq.gz, /Users/pditommaso/projects/demo/work/15/fea3e3ffbad40c235865305693fda0/001.reads_R2.trimmed.fastq.gz]
[sample_x, patient_y, /Users/pditommaso/projects/demo/work/15/fea3e3ffbad40c235865305693fda0/002.reads_R1.trimmed.fastq.gz, /Users/pditommaso/projects/demo/work/15/fea3e3ffbad40c235865305693fda0/002.reads_R2.trimmed.fastq.gz]
[sample_x, patient_y, /Users/pditommaso/projects/demo/work/15/fea3e3ffbad40c235865305693fda0/003.reads_R1.trimmed.fastq.gz, /Users/pditommaso/projects/demo/work/15/fea3e3ffbad40c235865305693fda0/003.reads_R2.trimmed.fastq.gz]
marchoeppner
@marchoeppner
Oct 01 2018 06:30
magical, great stuff, thanks!
Paolo Di Tommaso
@pditommaso
Oct 01 2018 06:31
:ok_hand:
@DoaneAS adding to what Evan already suggest, you can also specify SLURM --mem-per-cpu using clusterOptions instead of memory
@tobsecret what you are looking for/proposing is something similar to what proposed by this feature request nextflow-io/nextflow#725
Maxime Borry
@maxibor
Oct 01 2018 13:19
Hello all,
Is there a NF equivalent to the rules grouping in Snakemake that allows to submit a bunch of rules/processes together on a cluster ? (to avaid multiple job submission and too long waiting time in a cluster queue)
Félix C. Morency
@fmorency
Oct 01 2018 14:25
Not that I know of but I would also be interested in such feature
Tobias "Tobi" Schraink
@tobsecret
Oct 01 2018 15:27
Thanks! :pray: @pditommaso
Paolo Di Tommaso
@pditommaso
Oct 01 2018 15:27
you are welcome