Moved generate reports to custom folder as docker image needed

FROM nfcore/base:1.14

LABEL authors="chris.cheshire@crick.ac.uk" \

        description="Docker image containing all requirements for development of static reports"

# Install conda packages

COPY ./environment.yml /

RUN conda env create -f /environment.yml && conda clean -a

ENV PATH /opt/conda/envs/reporting/bin:$PATH

# conda env create -f environment.yml

name: reporting

channels:

  - conda-forge

  - bioconda

  - defaults

dependencies:

    # python version

    - python=3.8.3

    # conda packages

    - numpy=1.20.*

    - pandas=1.2.*

    - seaborn=0.11.*

    - pyranges=0.0.96

    - pysam=0.16.0.1

//

//  Utility functions used in nf-core DSL2 module files

//

//

// Extract name of software tool from process name using $task.process

//

def getSoftwareName(task_process) {

    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()

}

//

// Extract name of module from process name using $task.process

//

def getProcessName(task_process) {

    return task_process.tokenize(':')[-1]

}

//

// Function to initialise default values and to generate a Groovy Map of available options for nf-core modules

//

def initOptions(Map args) {

    def Map options = [:]

    options.args            = args.args ?: ''

    options.args2           = args.args2 ?: ''

    options.args3           = args.args3 ?: ''

    options.publish_by_meta = args.publish_by_meta ?: []

    options.publish_dir     = args.publish_dir ?: ''

    options.publish_files   = args.publish_files

    options.suffix          = args.suffix ?: ''

    return options

}

//

// Tidy up and join elements of a list to return a path string

//

def getPathFromList(path_list) {

    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }      // Remove empty entries

    paths     = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", "") } // Trim whitespace and trailing slashes

    return paths.join('/')

}

//

// Function to save/publish module results

//

def saveFiles(Map args) {

    def ioptions  = initOptions(args.options)

    def path_list = [ ioptions.publish_dir ?: args.publish_dir ]

    // Do not publish versions.yml unless running from pytest workflow

    if (args.filename.equals('versions.yml') && !System.getenv("NF_CORE_MODULES_TEST")) {

        return null

    }

    if (ioptions.publish_by_meta) {

        def key_list = ioptions.publish_by_meta instanceof List ? ioptions.publish_by_meta : args.publish_by_meta

        for (key in key_list) {

            if (args.meta && key instanceof String) {

                def path = key

                if (args.meta.containsKey(key)) {

                    path = args.meta[key] instanceof Boolean ? "${key}_${args.meta[key]}".toString() : args.meta[key]

                }

                path = path instanceof String ? path : ''

                path_list.add(path)

            }

        }

    }

    if (ioptions.publish_files instanceof Map) {

        for (ext in ioptions.publish_files) {

            if (args.filename.endsWith(ext.key)) {

                def ext_list = path_list.collect()

                ext_list.add(ext.value)

                return "${getPathFromList(ext_list)}/$args.filename"

            }

        }

    } else if (ioptions.publish_files == null) {

        return "${getPathFromList(path_list)}/$args.filename"

    }

}

include { initOptions; saveFiles; getSoftwareName; getProcessName } from '../common/functions'

include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'

params.options = [:]

options    = initOptions(params.options)

include { CALCULATE_PEAK_REPROD           } from "../modules/local/modules/calculate_peak_reprod/main" addParams( options: modules["calc_peak_repro"]   )

include { EXPORT_META                     } from "../modules/local/export_meta"                        addParams( options: modules["export_meta"]       )

include { EXPORT_META as EXPORT_META_CTRL } from "../modules/local/export_meta"                        addParams( options: modules["export_meta"]       )

include { GENERATE_REPORTS                } from "../modules/local/python/generate_reports"            addParams( options: modules["generate_reports"]  )

include { GENERATE_REPORTS                } from "../modules/local/modules/generate_reports/main"      addParams( options: modules["generate_reports"]  )

include { MULTIQC                         } from "../modules/local/multiqc"                            addParams( options: multiqc_options              )

/*