nextflow | A DSL for data-driven computational pipelines | BPM library

FROM python:3.8.9-slim 
LABEL 
authors="phil.ewels@scilifelab.se,erik.danielsson@scilifelab.se" \
  description="Docker image containing requirements for the nfcore tools"

# Do not pick up python packages from $HOME
ENV PYTHONNUSERSITE=1

nextflow.enable.dsl=2


params.publish_dir = System.getenv('TMPDIR') ?: './results'
params.publish_mode = 'copy'

check_params()


workflow {
    
    // your awesome workflow here
}

def check_params() {

    if( params.remove('help') ) {

input:
    [from ] [attributes]

ch1 = Channel.of( 'hello', 'world' )
ch2 = Channel.of( 1, 3, 5, 7, 9 )

params.foo = false
params.bar = false


process test {

    echo true

    input:
    val myval from ( params.

params.force = false

println("Force: ${params.force}")


process test {

    echo true

    when:
    params.force

    """
    echo "foo"
    """
}

nextflow run test.nf 
N E X T F L O W  ~  version 21.04.3
Launch

publishDir("${results_dir}/MY_PROC_RESULTS/", mode: "copy")

nextflow.enable.dsl=2

params.publish_dir = './results'

include { SUB_WORKFLOW_WF } from './SUB_WORKFLOW_WF_PROCS.nf'


workflow{
    
    SUB_WORKFLOW_W

params.input_csv = '/file/location/here/file.csv'

input_csv = file( params.input_csv)


process unique {

    input:
    path input_csv

    output:
    path 'full_template.csv' into template

    shell:
    '''
    awk 'BEGIN { FS=OFS=",

executor {
    queueSize = 1
}

nextflow.enable.dsl=2

process test {

    tag { "myval: ${myval}" }

    input:
    val myval

    """
    sleep 1
    """
}

workflow {

    myvals = Channel.of( 'A'..'Z' )

    tes

nextflow.enable.dsl=2

process foo {

    tag { sample }

    input:
    val sample

    output:
    path "${sample}.txt"

    """
    if [ "${sample}" == "s1" ] ; then
        (exit 1)
    fi
    if [ "${sample}" == "s2" ] ; then
        

proteins = Channel.fromPath( '/some/path/*.fa' ).collect()
executions = Channel.from(1, 2, 3, 4)

process blastThemAll {

  tag { "job ${num}" }

  input:
  val num from executions
  path query_file from proteins

  """
  find . -name '*.f