main.nf

// See the NOTICE file distributed with this work for additional information
// regarding copyright ownership.
//
// Licensed under the Apache License, Version 2.0 (the "License");
// you may not use this file except in compliance with the License.
// You may obtain a copy of the License at
//
//     http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software
// distributed under the License is distributed on an "AS IS" BASIS,
// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
// See the License for the specific language governing permissions and
// limitations under the License.
nextflow.enable.dsl=2

//default params
params.help = false

// mandatory params
params.webin_account = null  
params.webin_password = null
params.action = null
params.xml_output = null
params.context = null
params.mode = null
params.webinCli_dir = null
params.sender_email = null
params.rec_email = null
params.senderEmail_password = null
params.uuid = null
params.environment = null
params.transfer_output = "/"
params.transfer_flag = "/"


// Print usage
def helpMessage() {
  log.info """
        Usage:
        The typical command for running the pipeline is as follows:
        nextflow run pipeline/workflow/drag_and_drop_workflow/drag_and_drop_workflow.nf  --webin_account <webin account id> --webin_password <webin account password>  --context <reads/genome> --mode <validate/submit> --senderEmail_password <email password> --uuid <uuid> --environment <test/prod>

        Add the <sender_email> and <rec_email> value in the nextflow.config file

        Mandatory arguments:
        --webin_account                  The user webin account
        --webin_password                 The password of the webin account 
        --action                         Action to submit the metadata (add or modify) (Retrieved from the nextflow.config file)
        --xml_output                     The output of the metadata xml files (Retrieved from the nextflow.config file)
        --context                        Type of files
        --mode                           The type of file submission mode (submit or validate)
        --webinCli_dir                   The absolute path for the webin-cli file directory (Retrieved from the nextflow.config file)
        --sender_email                   Sender email address (Retrieved from the nextflow.config file)
        --rec_email                      Receiver email address(s) (Retrieved from the nextflow.config file)
        --senderEmail_password           Sender email password
        --uuid                           User specific access key for drag and drop tool
        --transfer_output                The absolute path for the transfer script output directory (the place house the files and the input metadata spreadsheet ) (Retrieved from the nextflow.config file)
        --environment                    The environment type (test/prod)

        Optional arguments:
        --help                         This usage statement.
        """
}

// Show help message
if (params.help) {
    helpMessage()
    exit 0
}

assert params.webin_account, "Parameter 'webin_account' is not specified"
assert params.webin_password, "Parameter 'webin_password' is not specified"
assert params.action, "Parameter 'action' is not specified"
assert params.xml_output, "Parameter 'xml_output' is not specified"
assert params.context, "Parameter 'context' is not specified"
assert params.mode, "Parameter 'mode' is not specified"
assert params.webinCli_dir, "Parameter 'webinCli_dir' is not specified"
assert params.sender_email, "Parameter 'sender_email' is not specified"
assert params.rec_email, "Parameter 'rec_email' is not specified"
assert params.senderEmail_password, "Parameter 'senderEmail_password' is not specified"
assert params.uuid, "Parameter 'uuid' is not specified"
assert params.transfer_output, "Parameter 'transfer_output' is not specified"
assert params.environment.toLowerCase() == 'test' || params.environment.toLowerCase() == 'prod' || params.environment.toLowerCase() == 'production',  "Parameter 'environment' is not specified, please specify one of the options(test or prod)"

// Import modules/subworkflows
include { dragDrop_workflow } from './workflow/dragDrop_workflow.nf'
// Run main workflow
workflow {
    main:
    dragDrop_workflow(params.webin_account, params.webin_password, params.action, params.xml_output, params.context, params.mode, params.webinCli_dir, params.sender_email, params.rec_email, params.senderEmail_password, params.uuid, params.transfer_output, params.transfer_flag, params.environment)
}