These are chat archives for nextflow-io/nextflow

3rd
Sep 2018
Luca Cozzuto
@lucacozzuto
Sep 03 2018 12:21
Hi @pditommaso, we have installed graphviz but I got an empty svg/png/pdf file when using -with-dag
Everything is ok when using dot/html
Paolo Di Tommaso
@pditommaso
Sep 03 2018 12:29
any suspicious message in the log file ?
Luca Cozzuto
@lucacozzuto
Sep 03 2018 12:29
no...
I tried to convert the dot file using dot but I got an error
dot -Tpdf graph.dot -o graph.pdf
Warning: graph.dot: syntax error in line 1 near 'graph'
the head of the dot file:
digraph graph {
p0 [shape=point,label="",fixedsize=true,width=0.1,xlabel="Channel.fromFilePairs"];
p1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="ifEmpty"];
p0 -> p1;

p1 [shape=circle,label="",fixedsize=true,width=0.1,xlabel="ifEmpty"];
p5 [label="trimReads"];
p1 -> p5 [label="read_files_for_trimming"];

p2 [shape=point,label="",fixedsize=true,width=0.1,xlabel="Channel.fromPath"];
Paolo Di Tommaso
@pditommaso
Sep 03 2018 12:31
I think you hit this
Luca Cozzuto
@lucacozzuto
Sep 03 2018 12:33
I'm sooooo happy :)
just changed the name worked. Thanks (PS: coffee time, you know where we are :) )
Paolo Di Tommaso
@pditommaso
Sep 03 2018 12:34
LOL
Issa Kehinde Salaam
@Issakenny
Sep 03 2018 12:40
Hi, I am new to nextflow, trying to install it from my terminal, using the cmd "curl -s https://get.nextflow.io | bash but nothing is happening. I have my curl updated but still no result. I tried alternative cmd "wget --no-check-certificate https://get.nextflow.io -O nextflow-install bash nextflow-install but received the error "connection to 172.20.4.1 :8080.. failed connection time out. Pls what can be the problem, cos I did not receive this error when installing 'Docker" kindly help out. Thanks
i am using Ubuntu 14.04
Issa Kehinde Salaam
@Issakenny
Sep 03 2018 14:27
I am using a portable wi-fi modem.
Paolo Di Tommaso
@pditommaso
Sep 03 2018 14:38
I see, I suggest to download it from GitHub
k-hench
@k-hench
Sep 03 2018 14:42

Hi folks,
I was wondering if somebody can point out how to fix a lading zero issue within nextflow:
I need to create a channel that includes all 24 chromosomes of my reference genome and that keeps the numbers consistently as two digit number.

I managed to solve the issue within groovy - but somehow my method breaks when applying it to a nextflow process:

LG_ids1 = Channel.from( 01..24 ).subscribe { println it.toString().padLeft( 2, '0' ) }
LG_id2 = Channel.from( 01..24 ).toString().padLeft( 2, '0' )

process as_script {
  echo true

  input:
  val input from LG_id2

  script:
  """
  echo ${input}
  """
}
k-hench
@k-hench
Sep 03 2018 15:27
@k-hench
I managed to solve my issue:
LG_id = Channel.from( 01..24 )

process transform {
  input:
  set val( id_in ) from LG_id

  output:
  val { id_in.toString().padLeft( 2, '0' ) } into transformed

  script:
  """
  """
}

process as_script {
  echo true

  input:
  val input from transformed

  script:
  """
  echo "LG"${input}
  """
}
Paolo Di Tommaso
@pditommaso
Sep 03 2018 15:36
string ranges are supported but limits need to have the same prefix, therefore you can do
Channel.from( ('01'..'09') + ('10'..'19') + ('20'..'24') )
or
chr = ('01'..'09') + ('10'..'19') + ('20'..'24')
LG_ids1 = Channel.from(chr)
LG_ids2 = Channel.from(chr)
k-hench
@k-hench
Sep 03 2018 15:57
cool - thanks, that's simple :)
Paolo Di Tommaso
@pditommaso
Sep 03 2018 15:58
nice