[MODIF] init DSL2

CITATIONS.md

+# nf-core/hic: Citations
+
+## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/)
+
+> Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031.
+
+## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/)
+
+> Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311.
+
+## Pipeline tools
+
+* [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
+
+* [MultiQC](https://www.ncbi.nlm.nih.gov/pubmed/27312411/)
+    > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924.
+
+## Software packaging/containerisation tools
+
+* [Anaconda](https://anaconda.com)
+    > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web.
+
+* [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/)
+    > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506.
+
+* [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/)
+    > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671.
+
+* [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241)
+
+* [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/)
+    > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675.

conf/modules.config

+/*
+========================================================================================
+    Config file for defining DSL2 per module options
+========================================================================================
+    Available keys to override module options:
+        args            = Additional arguments appended to command in module.
+        args2           = Second set of arguments appended to command in module (multi-tool modules).
+        args3           = Third set of arguments appended to command in module (multi-tool modules).
+        publish_dir     = Directory to publish results.
+        publish_by_meta = Groovy list of keys available in meta map to append as directories to "publish_dir" path
+                            If publish_by_meta = true                 - Value of ${meta['id']} is appended as a directory to "publish_dir" path
+                            If publish_by_meta = ['id', 'custompath'] - If "id" is in meta map and "custompath" isn't then "${meta['id']}/custompath/"
+                                                                        is appended as a directory to "publish_dir" path
+                            If publish_by_meta = false / null         - No directories are appended to "publish_dir" path
+        publish_files   = Groovy map where key = "file_ext" and value = "directory" to publish results for that file extension
+                            The value of "directory" is appended to the standard "publish_dir" path as defined above.
+                            If publish_files = null (unspecified)     - All files are published.
+                            If publish_files = false                  - No files are published.
+        suffix          = File name suffix for output files.
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    modules {
+        'fastqc' {
+            args = "--quiet"
+        }
+        'multiqc' {
+            args = ""
+        }
+    }
+}

lib/NfcoreTemplate.groovy

+//
+// This file holds several functions used within the nf-core pipeline template.
+//
+
+import org.yaml.snakeyaml.Yaml
+
+class NfcoreTemplate {
+
+    //
+    // Check AWS Batch related parameters have been specified correctly
+    //
+    public static void awsBatch(workflow, params) {
+        if (workflow.profile.contains('awsbatch')) {
+            // Check params.awsqueue and params.awsregion have been set if running on AWSBatch
+            assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!"
+            // Check outdir paths to be S3 buckets if running on AWSBatch
+            assert params.outdir.startsWith('s3:')       : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!"
+        }
+    }
+
+    //
+    // Check params.hostnames
+    //
+    public static void hostName(workflow, params, log) {
+        Map colors = logColours(params.monochrome_logs)
+        if (params.hostnames) {
+            try {
+                def hostname = "hostname".execute().text.trim()
+                params.hostnames.each { prof, hnames ->
+                    hnames.each { hname ->
+                        if (hostname.contains(hname) && !workflow.profile.contains(prof)) {
+                            log.info "=${colors.yellow}====================================================${colors.reset}=\n" +
+                                "${colors.yellow}WARN: You are running with `-profile $workflow.profile`\n" +
+                                "      but your machine hostname is ${colors.white}'$hostname'${colors.reset}.\n" +
+                                "      ${colors.yellow_bold}Please use `-profile $prof${colors.reset}`\n" +
+                                "=${colors.yellow}====================================================${colors.reset}="
+                        }
+                    }
+                }
+            } catch (Exception e) {
+                log.warn "[$workflow.manifest.name] Could not determine 'hostname' - skipping check. Reason: ${e.message}."
+            }
+        }
+    }
+
+    //
+    // Construct and send completion email
+    //
+    public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) {
+
+        // Set up the e-mail variables
+        def subject = "[$workflow.manifest.name] Successful: $workflow.runName"
+        if (!workflow.success) {
+            subject = "[$workflow.manifest.name] FAILED: $workflow.runName"
+        }
+
+        def summary = [:]
+        for (group in summary_params.keySet()) {
+            summary << summary_params[group]
+        }
+
+        def misc_fields = [:]
+        misc_fields['Date Started']              = workflow.start
+        misc_fields['Date Completed']            = workflow.complete
+        misc_fields['Pipeline script file path'] = workflow.scriptFile
+        misc_fields['Pipeline script hash ID']   = workflow.scriptId
+        if (workflow.repository) misc_fields['Pipeline repository Git URL']    = workflow.repository
+        if (workflow.commitId)   misc_fields['Pipeline repository Git Commit'] = workflow.commitId
+        if (workflow.revision)   misc_fields['Pipeline Git branch/tag']        = workflow.revision
+        misc_fields['Nextflow Version']           = workflow.nextflow.version
+        misc_fields['Nextflow Build']             = workflow.nextflow.build
+        misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp
+
+        def email_fields = [:]
+        email_fields['version']      = workflow.manifest.version
+        email_fields['runName']      = workflow.runName
+        email_fields['success']      = workflow.success
+        email_fields['dateComplete'] = workflow.complete
+        email_fields['duration']     = workflow.duration
+        email_fields['exitStatus']   = workflow.exitStatus
+        email_fields['errorMessage'] = (workflow.errorMessage ?: 'None')
+        email_fields['errorReport']  = (workflow.errorReport ?: 'None')
+        email_fields['commandLine']  = workflow.commandLine
+        email_fields['projectDir']   = workflow.projectDir
+        email_fields['summary']      = summary << misc_fields
+
+        // On success try attach the multiqc report
+        def mqc_report = null
+        try {
+            if (workflow.success) {
+                mqc_report = multiqc_report.getVal()
+                if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) {
+                    if (mqc_report.size() > 1) {
+                        log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one"
+                    }
+                    mqc_report = mqc_report[0]
+                }
+            }
+        } catch (all) {
+            if (multiqc_report) {
+                log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email"
+            }
+        }
+
+        // Check if we are only sending emails on failure
+        def email_address = params.email
+        if (!params.email && params.email_on_fail && !workflow.success) {
+            email_address = params.email_on_fail
+        }
+
+        // Render the TXT template
+        def engine       = new groovy.text.GStringTemplateEngine()
+        def tf           = new File("$projectDir/assets/email_template.txt")
+        def txt_template = engine.createTemplate(tf).make(email_fields)
+        def email_txt    = txt_template.toString()
+
+        // Render the HTML template
+        def hf            = new File("$projectDir/assets/email_template.html")
+        def html_template = engine.createTemplate(hf).make(email_fields)
+        def email_html    = html_template.toString()
+
+        // Render the sendmail template
+        def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit
+        def smail_fields           = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ]
+        def sf                     = new File("$projectDir/assets/sendmail_template.txt")
+        def sendmail_template      = engine.createTemplate(sf).make(smail_fields)
+        def sendmail_html          = sendmail_template.toString()
+
+        // Send the HTML e-mail
+        Map colors = logColours(params.monochrome_logs)
+        if (email_address) {
+            try {
+                if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') }
+                // Try to send HTML e-mail using sendmail
+                [ 'sendmail', '-t' ].execute() << sendmail_html
+                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-"
+            } catch (all) {
+                // Catch failures and try with plaintext
+                def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ]
+                if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) {
+                    mail_cmd += [ '-A', mqc_report ]
+                }
+                mail_cmd.execute() << email_html
+                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-"
+            }
+        }
+
+        // Write summary e-mail HTML to a file
+        def output_d = new File("${params.outdir}/pipeline_info/")
+        if (!output_d.exists()) {
+            output_d.mkdirs()
+        }
+        def output_hf = new File(output_d, "pipeline_report.html")
+        output_hf.withWriter { w -> w << email_html }
+        def output_tf = new File(output_d, "pipeline_report.txt")
+        output_tf.withWriter { w -> w << email_txt }
+    }
+
+    //
+    // Print pipeline summary on completion
+    //
+    public static void summary(workflow, params, log) {
+        Map colors = logColours(params.monochrome_logs)
+        if (workflow.success) {
+            if (workflow.stats.ignoredCount == 0) {
+                log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-"
+            } else {
+                log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed successfully, but with errored process(es) ${colors.reset}-"
+            }
+        } else {
+            hostName(workflow, params, log)
+            log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-"
+        }
+    }
+
+    //
+    // ANSII Colours used for terminal logging
+    //
+    public static Map logColours(Boolean monochrome_logs) {
+        Map colorcodes = [:]
+
+        // Reset / Meta
+        colorcodes['reset']      = monochrome_logs ? '' : "\033[0m"
+        colorcodes['bold']       = monochrome_logs ? '' : "\033[1m"
+        colorcodes['dim']        = monochrome_logs ? '' : "\033[2m"
+        colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m"
+        colorcodes['blink']      = monochrome_logs ? '' : "\033[5m"
+        colorcodes['reverse']    = monochrome_logs ? '' : "\033[7m"
+        colorcodes['hidden']     = monochrome_logs ? '' : "\033[8m"
+
+        // Regular Colors
+        colorcodes['black']      = monochrome_logs ? '' : "\033[0;30m"
+        colorcodes['red']        = monochrome_logs ? '' : "\033[0;31m"
+        colorcodes['green']      = monochrome_logs ? '' : "\033[0;32m"
+        colorcodes['yellow']     = monochrome_logs ? '' : "\033[0;33m"
+        colorcodes['blue']       = monochrome_logs ? '' : "\033[0;34m"
+        colorcodes['purple']     = monochrome_logs ? '' : "\033[0;35m"
+        colorcodes['cyan']       = monochrome_logs ? '' : "\033[0;36m"
+        colorcodes['white']      = monochrome_logs ? '' : "\033[0;37m"
+
+        // Bold
+        colorcodes['bblack']     = monochrome_logs ? '' : "\033[1;30m"
+        colorcodes['bred']       = monochrome_logs ? '' : "\033[1;31m"
+        colorcodes['bgreen']     = monochrome_logs ? '' : "\033[1;32m"
+        colorcodes['byellow']    = monochrome_logs ? '' : "\033[1;33m"
+        colorcodes['bblue']      = monochrome_logs ? '' : "\033[1;34m"
+        colorcodes['bpurple']    = monochrome_logs ? '' : "\033[1;35m"
+        colorcodes['bcyan']      = monochrome_logs ? '' : "\033[1;36m"
+        colorcodes['bwhite']     = monochrome_logs ? '' : "\033[1;37m"
+
+        // Underline
+        colorcodes['ublack']     = monochrome_logs ? '' : "\033[4;30m"
+        colorcodes['ured']       = monochrome_logs ? '' : "\033[4;31m"
+        colorcodes['ugreen']     = monochrome_logs ? '' : "\033[4;32m"
+        colorcodes['uyellow']    = monochrome_logs ? '' : "\033[4;33m"
+        colorcodes['ublue']      = monochrome_logs ? '' : "\033[4;34m"
+        colorcodes['upurple']    = monochrome_logs ? '' : "\033[4;35m"
+        colorcodes['ucyan']      = monochrome_logs ? '' : "\033[4;36m"
+        colorcodes['uwhite']     = monochrome_logs ? '' : "\033[4;37m"
+
+        // High Intensity
+        colorcodes['iblack']     = monochrome_logs ? '' : "\033[0;90m"
+        colorcodes['ired']       = monochrome_logs ? '' : "\033[0;91m"
+        colorcodes['igreen']     = monochrome_logs ? '' : "\033[0;92m"
+        colorcodes['iyellow']    = monochrome_logs ? '' : "\033[0;93m"
+        colorcodes['iblue']      = monochrome_logs ? '' : "\033[0;94m"
+        colorcodes['ipurple']    = monochrome_logs ? '' : "\033[0;95m"
+        colorcodes['icyan']      = monochrome_logs ? '' : "\033[0;96m"
+        colorcodes['iwhite']     = monochrome_logs ? '' : "\033[0;97m"
+
+        // Bold High Intensity
+        colorcodes['biblack']    = monochrome_logs ? '' : "\033[1;90m"
+        colorcodes['bired']      = monochrome_logs ? '' : "\033[1;91m"
+        colorcodes['bigreen']    = monochrome_logs ? '' : "\033[1;92m"
+        colorcodes['biyellow']   = monochrome_logs ? '' : "\033[1;93m"
+        colorcodes['biblue']     = monochrome_logs ? '' : "\033[1;94m"
+        colorcodes['bipurple']   = monochrome_logs ? '' : "\033[1;95m"
+        colorcodes['bicyan']     = monochrome_logs ? '' : "\033[1;96m"
+        colorcodes['biwhite']    = monochrome_logs ? '' : "\033[1;97m"
+
+        return colorcodes
+    }
+
+    //
+    // Does what is says on the tin
+    //
+    public static String dashedLine(monochrome_logs) {
+        Map colors = logColours(monochrome_logs)
+        return "-${colors.dim}----------------------------------------------------${colors.reset}-"
+    }
+
+    //
+    // nf-core logo
+    //
+    public static String logo(workflow, monochrome_logs) {
+        Map colors = logColours(monochrome_logs)
+        String.format(
+            """\n
+            ${dashedLine(monochrome_logs)}
+                                                    ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset}
+            ${colors.blue}        ___     __   __   __   ___     ${colors.green}/,-._.--~\'${colors.reset}
+            ${colors.blue}  |\\ | |__  __ /  ` /  \\ |__) |__         ${colors.yellow}}  {${colors.reset}
+            ${colors.blue}  | \\| |       \\__, \\__/ |  \\ |___     ${colors.green}\\`-._,-`-,${colors.reset}
+                                                    ${colors.green}`._,._,\'${colors.reset}
+            ${colors.purple}  ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset}
+            ${dashedLine(monochrome_logs)}
+            """.stripIndent()
+        )
+    }
+}

lib/Utils.groovy

+//
+// This file holds several Groovy functions that could be useful for any Nextflow pipeline
+//
+
+import org.yaml.snakeyaml.Yaml
+
+class Utils {
+
+    //
+    // When running with -profile conda, warn if channels have not been set-up appropriately
+    //
+    public static void checkCondaChannels(log) {
+        Yaml parser = new Yaml()
+        def channels = []
+        try {
+            def config = parser.load("conda config --show channels".execute().text)
+            channels = config.channels
+        } catch(NullPointerException | IOException e) {
+            log.warn "Could not verify conda channel configuration."
+            return
+        }
+
+        // Check that all channels are present
+        def required_channels = ['conda-forge', 'bioconda', 'defaults']
+        def conda_check_failed = !required_channels.every { ch -> ch in channels }
+
+        // Check that they are in the right order
+        conda_check_failed |= !(channels.indexOf('conda-forge') < channels.indexOf('bioconda'))
+        conda_check_failed |= !(channels.indexOf('bioconda') < channels.indexOf('defaults'))
+
+        if (conda_check_failed) {
+            log.warn "=============================================================================\n" +
+                "  There is a problem with your Conda configuration!\n\n" +
+                "  You will need to set-up the conda-forge and bioconda channels correctly.\n" +
+                "  Please refer to https://bioconda.github.io/user/install.html#set-up-channels\n" +
+                "  NB: The order of the channels matters!\n" +
+                "==================================================================================="
+        }
+    }
+
+    //
+    // Join module args with appropriate spacing
+    //
+    public static String joinModuleArgs(args_list) {
+        return ' ' + args_list.join(' ')
+    }
+}

lib/WorkflowHic.groovy

+//
+// This file holds several functions specific to the workflow/hic.nf in the nf-core/hic pipeline
+//
+
+class WorkflowHic {
+
+    //
+    // Check and validate parameters
+    //
+    public static void initialise(params, log) {
+        genomeExistsError(params, log)
+
+        if (!params.fasta) {
+            log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file."
+            System.exit(1)
+        }
+    }
+
+    //
+    // Get workflow summary for MultiQC
+    //
+    public static String paramsSummaryMultiqc(workflow, summary) {
+        String summary_section = ''
+        for (group in summary.keySet()) {
+            def group_params = summary.get(group)  // This gets the parameters of that particular group
+            if (group_params) {
+                summary_section += "    <p style=\"font-size:110%\"><b>$group</b></p>\n"
+                summary_section += "    <dl class=\"dl-horizontal\">\n"
+                for (param in group_params.keySet()) {
+                    summary_section += "        <dt>$param</dt><dd><samp>${group_params.get(param) ?: '<span style=\"color:#999999;\">N/A</a>'}</samp></dd>\n"
+                }
+                summary_section += "    </dl>\n"
+            }
+        }
+
+        String yaml_file_text  = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n"
+        yaml_file_text        += "description: ' - this information is collected when the pipeline is started.'\n"
+        yaml_file_text        += "section_name: '${workflow.manifest.name} Workflow Summary'\n"
+        yaml_file_text        += "section_href: 'https://github.com/${workflow.manifest.name}'\n"
+        yaml_file_text        += "plot_type: 'html'\n"
+        yaml_file_text        += "data: |\n"
+        yaml_file_text        += "${summary_section}"
+        return yaml_file_text
+    }
+
+    //
+    // Exit pipeline if incorrect --genome key provided
+    //
+    private static void genomeExistsError(params, log) {
+        if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) {
+            log.error "=============================================================================\n" +
+                "  Genome '${params.genome}' not found in any config files provided to the pipeline.\n" +
+                "  Currently, the available genome keys are:\n" +
+                "  ${params.genomes.keySet().join(", ")}\n" +
+                "==================================================================================="
+            System.exit(1)
+        }
+    }
+}

lib/WorkflowMain.groovy

+//
+// This file holds several functions specific to the main.nf workflow in the nf-core/hic pipeline
+//
+
+class WorkflowMain {
+
+    //
+    // Citation string for pipeline
+    //
+    public static String citation(workflow) {
+        return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" +
+            // TODO nf-core: Add Zenodo DOI for pipeline after first release
+            //"* The pipeline\n" +
+            //"  https://doi.org/10.5281/zenodo.XXXXXXX\n\n" +
+            "* The nf-core framework\n" +
+            "  https://doi.org/10.1038/s41587-020-0439-x\n\n" +
+            "* Software dependencies\n" +
+            "  https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md"
+    }
+
+    //
+    // Print help to screen if required
+    //
+    public static String help(workflow, params, log) {
+        def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker"
+        def help_string = ''
+        help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs)
+        help_string += NfcoreSchema.paramsHelp(workflow, params, command)
+        help_string += '\n' + citation(workflow) + '\n'
+        help_string += NfcoreTemplate.dashedLine(params.monochrome_logs)
+        return help_string
+    }
+
+    //
+    // Print parameter summary log to screen
+    //
+    public static String paramsSummaryLog(workflow, params, log) {
+        def summary_log = ''
+        summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs)
+        summary_log += NfcoreSchema.paramsSummaryLog(workflow, params)
+        summary_log += '\n' + citation(workflow) + '\n'
+        summary_log += NfcoreTemplate.dashedLine(params.monochrome_logs)
+        return summary_log
+    }
+
+    //
+    // Validate parameters and print summary to screen
+    //
+    public static void initialise(workflow, params, log) {
+        // Print help to screen if required
+        if (params.help) {
+            log.info help(workflow, params, log)
+            System.exit(0)
+        }
+
+        // Validate workflow parameters via the JSON schema
+        if (params.validate_params) {
+            NfcoreSchema.validateParameters(workflow, params, log)
+        }
+
+        // Print parameter summary log to screen
+        log.info paramsSummaryLog(workflow, params, log)
+
+        // Check that conda channels are set-up correctly
+        if (params.enable_conda) {
+            Utils.checkCondaChannels(log)
+        }
+
+        // Check AWS batch settings
+        NfcoreTemplate.awsBatch(workflow, params)
+
+        // Check the hostnames against configured profiles
+        NfcoreTemplate.hostName(workflow, params, log)
+
+        // Check input has been provided
+        if (!params.input) {
+            log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'"
+            System.exit(1)
+        }
+    }
+
+    //
+    // Get attribute from genome config file e.g. fasta
+    //
+    public static String getGenomeAttribute(params, attribute) {
+        def val = ''
+        if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) {
+            if (params.genomes[ params.genome ].containsKey(attribute)) {
+                val = params.genomes[ params.genome ][ attribute ]
+            }
+        }
+        return val
+    }
+}

modules.json

+{
+    "name": "nf-core/hic",
+    "homePage": "https://github.com/nf-core/hic",
+    "repos": {
+        "nf-core/modules": {
+            "fastqc": {
+                "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
+            },
+            "multiqc": {
+                "git_sha": "e937c7950af70930d1f34bb961403d9d2aa81c7d"
+            }
+        }
+    }
+}

modules/local/bowtie2_end_to_end.nf

+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options    = initOptions(params.options)
+
+process bowtie2_end_to_end {
+   tag "$sample"
+   label 'process_medium'
+   publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping/bwt2_end2end" : params.outdir },
+              saveAs: { filename -> if (params.save_aligned_intermediates) filename }, mode: params.publish_dir_mode
+
+   input:
+   tuple val(sample), path(reads)
+   path index
+
+   output:
+   tuple val(sample), path("${prefix}_unmap.fastq"), emit: unmapped_end_to_end
+   tuple val(sample), path("${prefix}.bam"), emit: end_to_end_bam
+
+   script:
+   prefix = reads.toString() - ~/(\.fq)?(\.fastq)?(\.gz)?$/
+   def bwt2_opts = params.bwt2_opts_end2end
+   if (!params.dnase){
+   """
+   INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
+   bowtie2 --rg-id BMG --rg SM:${prefix} \\
+	${bwt2_opts} \\
+	-p ${task.cpus} \\
+	-x \${INDEX} \\
+	--un ${prefix}_unmap.fastq \\
+ 	-U ${reads} | samtools view -F 4 -bS - > ${prefix}.bam
+   """
+   }else{
+   """
+   INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
+   bowtie2 --rg-id BMG --rg SM:${prefix} \\
+	${bwt2_opts} \\
+	-p ${task.cpus} \\
+	-x \${INDEX} \\
+	--un ${prefix}_unmap.fastq \\
+ 	-U ${reads} > ${prefix}.bam
+   """
+   }
+}

modules/local/bowtie2_merge_mapping_steps.nf

+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options    = initOptions(params.options)
+
+process bowtie2_merge_mapping_steps{
+      tag "$prefix = $bam1 + $bam2"
+      label 'process_medium'
+      publishDir "${params.outdir}/hicpro/mapping", mode: params.publish_dir_mode,
+   	      saveAs: { filename -> if (params.save_aligned_intermediates && filename.endsWith("stat")) "stats/$filename"
+			else if (params.save_aligned_intermediates) filename}
+
+      input:
+      tuple val(prefix), path(bam1), path(bam2) 
+
+      output:
+      tuple val(sample), path("${prefix}_bwt2merged.bam"), emit:bwt2_merged_bam
+      tuple val(oname), path("${prefix}.mapstat"), emit:all_mapstat
+
+      script:
+      sample = prefix.toString() - ~/(_R1|_R2)/
+      tag = prefix.toString() =~/_R1/ ? "R1" : "R2"
+      oname = prefix.toString() - ~/(\.[0-9]+)$/
+      """
+      samtools merge -@ ${task.cpus} \\
+    	             -f ${prefix}_bwt2merged.bam \\
+                     ${bam1} ${bam2}
+
+      samtools sort -@ ${task.cpus} -m 800M \\
+      	            -n  \\
+	            -o ${prefix}_bwt2merged.sorted.bam \\
+	            ${prefix}_bwt2merged.bam
+
+      mv ${prefix}_bwt2merged.sorted.bam ${prefix}_bwt2merged.bam
+
+      echo "## ${prefix}" > ${prefix}.mapstat
+      echo -n "total_${tag}\t" >> ${prefix}.mapstat
+      samtools view -c ${prefix}_bwt2merged.bam >> ${prefix}.mapstat
+      echo -n "mapped_${tag}\t" >> ${prefix}.mapstat
+      samtools view -c -F 4 ${prefix}_bwt2merged.bam >> ${prefix}.mapstat
+      echo -n "global_${tag}\t" >> ${prefix}.mapstat
+      samtools view -c -F 4 ${bam1} >> ${prefix}.mapstat
+      echo -n "local_${tag}\t"  >> ${prefix}.mapstat
+      samtools view -c -F 4 ${bam2} >> ${prefix}.mapstat
+      """
+}

modules/local/bowtie2_on_trimmed_reads.nf

+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options    = initOptions(params.options)
+
+process bowtie2_on_trimmed_reads {
+   tag "$sample"
+   label 'process_medium'
+   publishDir path: { params.save_aligned_intermediates ? "${params.outdir}/mapping/bwt2_trimmed" : params.outdir },
+   	      saveAs: { filename -> if (params.save_aligned_intermediates) filename }, mode: params.publish_dir_mode
+
+   when:
+   !params.dnase
+
+   input:
+   tuple val(sample), path(reads) 
+   path index 
+
+   output:
+   tuple val(sample), path("${prefix}_trimmed.bam"), emit:trimmed_bam
+
+   script:
+   prefix = reads.toString() - ~/(_trimmed)?(\.fq)?(\.fastq)?(\.gz)?$/
+   """
+   INDEX=`find -L ./ -name "*.rev.1.bt2" | sed 's/.rev.1.bt2//'`
+   bowtie2 --rg-id BMG --rg SM:${prefix} \\
+           ${params.bwt2_opts_trimmed} \\
+           -p ${task.cpus} \\
+           -x \${INDEX} \\
+           -U ${reads} | samtools view -bS - > ${prefix}_trimmed.bam
+   """
+}

modules/local/build_contact_maps.nf

+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options    = initOptions(params.options)
+
+process build_contact_maps{
+   tag "$sample - $mres"
+   label 'process_highmem'
+   publishDir "${params.outdir}/hicpro/matrix/raw", mode: params.publish_dir_mode
+
+   when:
+   !params.skip_maps && params.hicpro_maps
+
+   input:
+   tuple val(sample), path(vpairs), val(mres) 
+   path chrsize 
+
+   output:
+   tuple val(sample), val(mres), path("*.matrix"), path("*.bed"), emit: raw_maps_4cool
+   
+   script:
+   """
+   build_matrix --matrix-format upper  --binsize ${mres} --chrsizes ${chrsize} --ipath ${vpairs} --oprefix ${sample}_${mres}
+   """
+}

modules/local/combine_mates.nf

+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options    = initOptions(params.options)
+
+process combine_mates{
+   tag "$sample = $r1_prefix + $r2_prefix"
+   label 'process_low'
+   publishDir "${params.outdir}/hicpro/mapping", mode: params.publish_dir_mode,
+   	      saveAs: {filename -> filename.endsWith(".pairstat") ? "stats/$filename" : "$filename"}
+
+   input:
+   tuple val(sample), path(aligned_bam) 
+
+   output:
+   tuple val(oname), path("${sample}_bwt2pairs.bam"), emit:paired_bam
+   tuple val(oname), path("*.pairstat"), emit:all_pairstat
+
+   script:
+   r1_bam = aligned_bam[0]
+   r1_prefix = r1_bam.toString() - ~/_bwt2merged.bam$/
+   r2_bam = aligned_bam[1]
+   r2_prefix = r2_bam.toString() - ~/_bwt2merged.bam$/
+   oname = sample.toString() - ~/(\.[0-9]+)$/
+
+   def opts = "-t"
+   if (params.keep_multi) {
+     opts="${opts} --multi"
+   }else if (params.min_mapq){
+     opts="${opts} -q ${params.min_mapq}"
+   }
+   """
+   mergeSAM.py -f ${r1_bam} -r ${r2_bam} -o ${sample}_bwt2pairs.bam ${opts}
+   """
+}

modules/local/compartment_calling.nf

+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options    = initOptions(params.options)
+
+process compartment_calling {
+  tag "$sample - $res"
+  label 'process_medium'
+  publishDir "${params.outdir}/compartments", mode: 'copy'
+
+  when:
+  !params.skip_compartments
+
+  input:
+  tuple val(sample), val(res), path(cool), val(r) 
+  path(fasta) 
+  path(chrsize) 
+
+  output:
+  path("*compartments*") optional true, emit:out_compartments
+
+  script:
+  """
+  cooltools genome binnify --all-names ${chrsize} ${res} > genome_bins.txt
+  cooltools genome gc genome_bins.txt ${fasta} > genome_gc.txt 
+  cooltools call-compartments --contact-type cis -o ${sample}_compartments ${cool}
+  awk -F"\t" 'NR>1{OFS="\t"; if(\$6==""){\$6=0}; print \$1,\$2,\$3,\$6}' ${sample}_compartments.cis.vecs.tsv | sort -k1,1 -k2,2n > ${sample}_compartments.cis.E1.bedgraph
+  """
+}

modules/local/converts_to_pairs.nf

+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options    = initOptions(params.options)
+
+process convert_to_pairs {
+   tag "$sample"
+   label 'process_medium'
+
+   when:
+   !params.skip_maps
+
+   input:
+   tuple val(sample), path(vpairs) 
+   path chrsize 
+
+   output:
+   tuple val(sample), path("*.txt.gz"), emit: cool_build_zoom
+
+   script:
+   """
+   ## chr/pos/strand/chr/pos/strand
+   awk '{OFS="\t";print \$1,\$2,\$3,\$5,\$6,\$4,\$7}' $vpairs > contacts.txt
+   gzip contacts.txt
+   """
+}

modules/local/cooler_balance.nf

+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options    = initOptions(params.options)
+
+process cooler_balance {
+  tag "$sample - ${res}"
+  label 'process_medium'
+
+  publishDir "${params.outdir}/contact_maps/", mode: 'copy',
+              saveAs: {filename -> filename.endsWith(".cool") ? "norm/cool/$filename" : "norm/txt/$filename"}
+
+  when:
+  !params.skip_balancing
+
+  input:
+  tuple val(sample), val(res), path(cool) 
+  path chrsize 
+
+  output:
+  tuple val(sample), val(res), path("${sample}_${res}_norm.cool"), emit:balanced_cool_maps
+  path("${sample}_${res}_norm.txt"), emit:norm_txt_maps
+
+  script:
+  """
+  cp ${cool} ${sample}_${res}_norm.cool
+  cooler balance ${sample}_${res}_norm.cool -p ${task.cpus} --force
+  cooler dump ${sample}_${res}_norm.cool --balanced --na-rep 0 | awk '{OFS="\t"; print \$1+1,\$2+1,\$4}' > ${sample}_${res}_norm.txt
+  """
+}

modules/local/cooler_raw.nf

+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options    = initOptions(params.options)
+
+process cooler_raw {
+  tag "$sample - ${res}"
+  label 'process_medium'
+
+  publishDir "${params.outdir}/contact_maps/", mode: 'copy',
+              saveAs: {filename -> filename.endsWith(".cool") ? "raw/cool/$filename" : "raw/txt/$filename"}
+
+  input:
+  tuple val(sample), path(contacts), val(res) 
+  path chrsize 
+
+  output:
+  tuple val(sample), val(res), path("*cool"), emit:raw_cool_maps
+  tuple path("*.bed"), path("${sample}_${res}.txt"), emit:raw_txt_maps
+
+  script:
+  """
+  cooler makebins ${chrsize} ${res} > ${sample}_${res}.bed
+  cooler cload pairs -c1 2 -p1 3 -c2 4 -p2 5 ${sample}_${res}.bed ${contacts} ${sample}_${res}.cool
+  cooler dump ${sample}_${res}.cool | awk '{OFS="\t"; print \$1+1,\$2+1,\$3}' > ${sample}_${res}.txt
+  """
+}

modules/local/cooler_zoomify.nf

+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options    = initOptions(params.options)
+
+process cooler_zoomify {
+   tag "$sample"
+   label 'process_medium'
+   publishDir "${params.outdir}/contact_maps/norm/mcool", mode: 'copy'
+
+   when:
+   !params.skip_mcool
+
+   input:
+   tuple val(sample), path(contacts)  
+   path chrsize 
+
+   output:
+   path("*mcool"), emit:mcool_maps
+
+   script:
+   """
+   cooler makebins ${chrsize} ${params.res_zoomify} > bins.bed
+   cooler cload pairs -c1 2 -p1 3 -c2 4 -p2 5 bins.bed ${contacts} ${sample}.cool
+   cooler zoomify --nproc ${task.cpus} --balance ${sample}.cool
+   """
+}

modules/local/dist_decay.nf

+// Import generic module functions
+include { initOptions; saveFiles; getSoftwareName } from './functions'
+
+params.options = [:]
+options    = initOptions(params.options)
+
+process dist_decay {
+  tag "$sample"
+  label 'process_medium'
+  publishDir "${params.outdir}/dist_decay", mode: 'copy'
+
+  when:
+  !params.skip_dist_decay
+
+  input:
+  tuple val(sample), val(res), path(maps), val(r) 
+  
+  output:
+  path("*_distcount.txt")
+  path("*.png")
+
+
+  script:
+  """
+  hicPlotDistVsCounts --matrices ${maps} \
+                      --plotFile ${maps.baseName}_distcount.png \
+  		      --outFileData ${maps.baseName}_distcount.txt
+  """
+}