rsuchecki

params.pipes = false //Alternative sytax for DSL2 workflows
params.nested = false //if not pipes, use the nested workflow syntax
  
workflow {
  /*
  For demonstration purposes we are comparing 3 different 
  syntax styles of workflow composition
  These can also be mixed. 
  The 'pipes' work best when each process has only one input (which may be a tuple of multiple elements)
  */

rsuchecki

# 1.install gource using HomeBrew
$ brew install gource

# 2.install avconv
git clone git://git.libav.org/libav.git
cd libav 
# it will take 3-5 minutes to complie, be patient.
./configure --disable-yasm
make && make install 

rsuchecki

feedback_ch = Channel.create()
input_ch = Channel.from([1,2,3,4,5,6,7]).merge( feedback_ch ) //.until{count++ > 10 }
feedback_ch << 1

process build {
  input: tuple val(v), val(u) from input_ch
  output: val(y) into feedback_ch
  
  exec:
  y = v+u

rsuchecki

# Ensure each new screen ends up with it's own history file bind c screen bash -ic 'HISTFILE=~/.bash_history.${WINDOW} bash'
bind c screen bash -ic 'HISTFILE=~/.bash_history.${WINDOW} bash -l'
bind ^C screen bash -ic 'HISTFILE=~/.bash_history.${WINDOW} bash -l'

# some default tabs
screen -t "bash" bash -l
#termcapinfo xterm ti@:te@

# Bind F8 and F9 to previous and next screen window
bindkey -k k8 prev

rsuchecki

rsuchecki

channelsQ = (Channel.from('World', 'Mundo').into(2) as Queue)

process foo {
  input: val x from ( channelsQ.poll() )
  exec: println "Foo says: Hello ${x}"
}

process bar {
  input: val x from ( channelsQ.poll() )
  exec: println "Bar says: Hello ${x}"

rsuchecki

flatMap { flag, files ->
  files instanceof Collection ? {def ret = []; files.each {ret << [flag, it] }; ret}() : [[flag, files]]
}

rsuchecki

task_id	hash	native_id	name	status	exit	submit	duration	realtime	%cpu	peak_rss	peak_vmem	rchar	wchar
3	93/5be529	25680649	fetchRemoteDataFromEnsemblPlants ([species:Arabidopsis_thaliana, version:TAIR10, source:https://plants.ensembl.org/Arabidopsis_thaliana, release:39, shortName:TAIR])	CACHED	0	2019-05-13 22:16:05.866	34.5s	26.2s	1.1%	9.2 MB	199.7 MB	9.5 MB	41.5 MB
4	b6/e465bf	25680659	fetchRemoteDataFromEnsemblPlants ([species:Hordeum_vulgare, version:IBSC_v2, source:https://plants.ensembl.org/Hordeum_vulgare, release:43, shortName:Barley])	CACHED	0	2019-05-13 22:19:06.207	34.7s	31.3s	2.4%	9.3 MB	199.7 MB	18 MB	145.4 MB
6	16/ad4f35	25680648	fetchRemoteDataFromEnsemblPlants ([species:Oryza_sativa, version:IRGSP-1.0, source:https://plants.ensembl.org/Oryza_sativa, release:39, shortName:IRGSP])	CACHED	0	2019-05-13 22:16:05.777	34.5s	26.9s	1.1%	9.3 MB	199.7 MB	9.7 MB	34.6 MB
3	be/dde3f8	25680802	fetchRemoteDataFromEnsemblPlants ([species:Brachypodium_distachyon, version:Brachypodium_distachyon_v3.0, source:http

rsuchecki

def args = ['-arg 1', '-arg 2', '-arg 3', '-arg 4']

comb = []
1.upto(args.size()) {
    [args].multiply(it).eachCombination { list ->
      if(list.size() == 1 || (1..<list.size()).every { list[it - 1] < list[it] }) {
           comb << list
      }
    }
}

rsuchecki

bars = ['bar1', 'bar2']
process foo {
  tag "${bar}"
  label "${bar}"

  input:
    each bar from bars

  exec:
    println ("Current: "+bar)