script.nf

#! /usr/bin/env nextflow

// Copyright (C) 2017 IARC/WHO

// This program is free software: you can redistribute it and/or modify
// it under the terms of the GNU General Public License as published by
// the Free Software Foundation, either version 3 of the License, or
// (at your option) any later version.

// This program is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
// GNU General Public License for more details.

// You should have received a copy of the GNU General Public License
// along with this program.  If not, see <http://www.gnu.org/licenses/>.

params.help = null

log.info ""
log.info "--------------------------------------------------------"
log.info "  <PROGRAM_NAME> <VERSION>: <SHORT DESCRIPTION>         "
log.info "--------------------------------------------------------"
log.info "Copyright (C) IARC/WHO"
log.info "This program comes with ABSOLUTELY NO WARRANTY; for details see LICENSE"
log.info "This is free software, and you are welcome to redistribute it"
log.info "under certain conditions; see LICENSE for details."
log.info "--------------------------------------------------------"
log.info ""

if (params.help) {
    log.info "--------------------------------------------------------"
    log.info "  USAGE                                                 "
    log.info "--------------------------------------------------------"
    log.info ""
    log.info "nextflow run iarcbioinfo/template-nf [-with-docker] [OPTIONS]"
    log.info ""
    log.info "Mandatory arguments:"
    log.info "--<OPTION>                      <TYPE>                      <DESCRIPTION>"
    log.info ""
    log.info "Optional arguments:"
    log.info "--<OPTION>                      <TYPE>                      <DESCRIPTION>"
    log.info ""
    log.info "Flags:"
    log.info "--<FLAG>                                                    <DESCRIPTION>"
    log.info ""
    exit 0
} else {
/* Software information */
log.info "help:                               ${params.help}"
}

str = Channel.from('hello', 'hola', 'bonjour', 'ciao')

process printHello {

    input:
    val str

    output:
    stdout into result

    shell:
    '''
    echo !{str}
    '''
}

result.println()