main.nf

// Using DSL-2
nextflow.enable.dsl=2
import groovy.json.JsonSlurper

log.info """\
         E X O M E - R N A S E Q - N F   P I P E L I N E
         ===================================
         NF version   : $nextflow.version
         runName      : $workflow.runName
         username     : $workflow.userName
         configs      : $workflow.configFiles
         profile      : $workflow.profile
         cmd line     : $workflow.commandLine
         start time   : $workflow.start
         projectDir   : $workflow.projectDir
         launchDir    : $workflow.launchDir
         workdDir     : $workflow.workDir
         homeDir      : $workflow.homeDir
         """
         .stripIndent()



//import workflows

include {RNAseq_only} from './workflows/RNAseq_only.nf'
include {RNAseq_multiple_libs} from './workflows/RNAseq_multiple_libs.nf'
include {Exome_only_WF} from './workflows/Exome_only_WF.nf'
include {Tumor_multiple_libs} from './workflows/Tumor_multiple_libs.nf'
include {Tumor_Normal_WF} from './workflows/Tumor_Normal_WF.nf'
include {Tumor_Normal_RNAseq_WF} from './workflows/Tumor_Normal_RNAseq_WF.nf'
include {Tumor_RNAseq_WF} from './workflows/Tumor_RNAseq_WF.nf'
include {Mouse_RNA} from './workflows/Mouse_RNA.nf'


// Launch workflow by checking the samplesheet availability
workflow {


if (fileExists("Exome.csv")) {
    Exome_only_WF()
} else if (fileExists("Tumor_lib.csv")) {
    Tumor_multiple_libs()
} else if (fileExists("Tumor_RNAseq_Normal.csv")) {
    Tumor_Normal_RNAseq_WF()
} else if (fileExists("RNAseq.csv")) {
    RNAseq_only()
} else if (fileExists("RNA_lib.csv")) {
    RNAseq_multiple_libs()
} else if (fileExists("Tumor_Normal.csv")) {
    Tumor_Normal_WF()
} else if (fileExists("Tumor_RNAseq.csv")) {
    Tumor_RNAseq_WF()
} else if (fileExists("mouse_rnaseq.csv")) {
    Mouse_RNA()
} else {
    println("No workflow to run. Required file is missing.")
}


/*
get_project_list()
*/
}
/*
process get_project_list {
    output:
    path "list.txt"

    script:
    """
    python3 /data/khanlab/projects/processed_DATA/nf_samplesheets/projectlist.py /data/khanlab/projects/processed_DATA/nf_samplesheets/PAXCPA_PAXCPA.csv > list.txt
    """
}
*/


workflow.onComplete {


    if (workflow.success) {

        if (workflow.profile == "biowulf_mouse_RNA_slurm") {
            // Special handling for the mouse workflow
            def successFile = new File("${workflow.launchDir}/completed.txt")
            successFile.createNewFile()

            def fullMessage = "Mouse RNAseq workflow completed successfully. Results are located at ${workflow.launchDir}"
            sendMail(to: "${workflow.userName}@mail.nih.gov", subject: 'Mouse RNAseq Workflow Complete', body: fullMessage, mimeType: 'text/plain')

        } else {


            def successFile = new File("${workflow.launchDir}/successful.txt")
            successFile.createNewFile()

            def htmlFile = new File("${workflow.launchDir}/qc/genotyping.html")
            def htmlContent = htmlFile.text
            def fullMessage = "${htmlContent}"


            //sendMail(to: "${workflow.userName}@mail.nih.gov" , subject: 'khanlab ngs-pipeline execution successful', body: fullMessage, mimeType: 'text/html')

            sendMail(to: "${workflow.userName}@mail.nih.gov" , cc: 'wenxi@mail.nih.gov, gangalapudiv2@mail.nih.gov,' , subject: 'khanlab ngs-pipeline execution successful', body: fullMessage, mimeType: 'text/html')
        }

    } else {
        fullMessage = "Workflow completed with errors. Error log is located at ${workflow.launchDir}"
        sendMail(to: "${workflow.userName}@mail.nih.gov" , cc: 'gangalapudiv2@mail.nih.gov', subject: 'khanlab ngs-pipeline execution failed', body: fullMessage, mimeType: 'text/html')
    }

}


def fileExists(String filePath) {
    new File(filePath).exists()
}